Ubuntu Manpage: vsearch — chimera detection, clustering, dereplication, masking, pairwise alignment, searching, shuffling

NAME

       vsearch — chimera detection, clustering, dereplication, masking, pairwise alignment, searching, shuffling
       and sorting of amplicons from metagenomic projects.

SYNOPSIS

       Chimera detection:
              vsearch --uchime_denovo fastafile (--chimeras | --nonchimeras | --uchimealns | --uchimeout)
              outputfile [options]

              vsearch --uchime_ref fastafile (--chimeras | --nonchimeras | --uchimealns | --uchimeout)
              outputfile --db fastafile [options]

       Clustering:
              vsearch (--cluster_fast | --cluster_size | --cluster_smallmem) fastafile (--alnout | --blast6out |
              --centroids | --clusters | --msaout | --samout | --uc | --userout) outputfile --id real [options]

       Dereplication:
              vsearch --derep_fulllength fastafile (--output | --uc) outputfile [options]

       Masking:
              vsearch --maskfasta fastafile --output outputfile [options]

       Pairwise alignment:
              vsearch --allpairs_global fastafile (--alnout | --blast6out | --matched | --notmatched | --samout
              | --uc | --userout) outputfile (--acceptall | --id real) [options]

       Searching:
              vsearch --usearch_global fastafile --db fastafile (--alnout | --blast6out | --samout | --uc |
              --userout) outputfile --id real [options]

       Shuffling:
              vsearch --shuffle fastafile --output outputfile [options]

       Sorting:
              vsearch (--sortbylength | --sortbysize) fastafile --output outputfile [options]

DESCRIPTION

Environmental or clinical molecular diversity studies generate large volumes of amplicons (e.g. SSU-rRNA
sequences) that need to be checked for chimeras, dereplicated, masked, sorted, searched, clustered or
compared to reference sequences. The aim of vsearch is to offer a all-in-one open source tool to perform
these tasks, using optimized algorithm implementations and harvesting the full potential of modern
computers, thus providing fast and accurate data processing.

Comparing nucleotide sequences is at the core of vsearch. To speed up comparisons, vsearch implements an
extremely fast implementation of the Needleman-Wunsch algorithm, making use of the Streaming SIMD
Extensions (SSE2) of modern x86-64 CPUs. If SSE2 instructions are not available, vsearch exits with an
error message. For comparisons involving sequences longer than 5,000 nucleotides, vsearch uses a slower
alignment method with smaller memory requirements.

Input
vsearch input is a fasta file containing one or several nucleotide sequences. For each sequence, the
sequence identifier is defined as the string comprised between the ">" symbol and the first space, or the
end of the line, whichever comes first. Additionally, if the line starts with ">[;]size=integer;label",
contains ">label;size=integer;label" or ends with ">label;size=integer[;]", vsearch will remove the
pattern [;]size=integer[;] from the header and interpret integer as the number of occurrences (or
abundance) of the sequence in the study. That abundance information is used or created during chimera
detection, clustering, dereplication, sorting and searching.

The nucleotide sequence is defined as a string of IUPAC symbols (ACGTURYSWKMDBHVN), starting after the
end of the identifier line and ending before the next identifier line, or the file end. vsearch silently
ignores ascii characters 9 to 13, and exits with an error message if ascii characters 0 to 8, 14 to 31,
"." or "-" are present. All other ascii or non-ascii characters are stripped and complained about in a
non-blocking warning message.

vsearch operations are case insensitive, except when soft masking is activated. When using clustering,
masking or searching commands, the case is important if soft masking is used. Soft masking is specified
with the options "--dbmask soft" (for searching) or "--qmask soft" (for searching, clustering and
masking). When using soft masking, lower case letters indicate masked symbols, while upper case letters
indicate regular symbols. Masked symbols are never included in the unique k-mers used in searching. When
soft masking is not activated, all letters are converted to upper case internally and used in result
files.

When comparing sequences during chimera detection, dereplication, searching and clustering, T and U are
considered identical, regardless of their case. If two symbols are not identical, their alignment will
result in the negative mismatch score (default -4), except if one or both of the symbols are ambiguous
(RYSWKMDBHVN) in which case the score is zero. Alignment of two identical ambiguous symbols (e.g. R vs R)
also receives a score of zero.

vsearch can be compiled to accepted compressed fasta files as input (gz and bzip2 formats). On the other
hand, special files like pipes, named pipes, or sockets cannot be used as input. To present a progress
indicator, vsearch needs to seek to the end of filename to find its length. Consequently, filename must
be a regular file, not a stream.

Options
vsearch recognizes a large number of command-line options. For easier navigation, options are grouped
below by theme (chimera detection, clustering, dereplication, masking, shuffling, sorting, and
searching). We start with general options that apply to all themes.

General options:

--fasta_width positive integer
Fasta files produced by vsearch are wrapped (sequences are written on lines of integer
nucleotides, 80 by default). Set that value to 0 to eliminate the wrapping.

--help Display a short help and exit.

--log filename
Write messages to the specified log file. Information written includes program version,
amount of memory available, number of cores and command line options. The start and
finish times are also recorded as well as the elapsed time. The maximum amount of memory
consumed is included. The different commands will usually also write some information
about their results. Both fatal, warning and informational messages are written.

--maxseqlength positive integer
All vsearch operations will discard sequences of length equal or greater than integer
(50,000 nucleotides by default).

--minseqlength positive integer
All vsearch operations will discard sequences of length smaller than integer (1
nucleotide by default for sorting or shuffling, 32 nucleotides for clustering,
dereplication or searching).

--notrunclabels
Do not truncate sequence labels at first space, use the full header in output files.

--quiet Suppress all output to stdout and stdout except for warnings and fatal error messages.

--version
Output version information and exit.

Chimera detection options:

Chimera detection is based on a scoring function controlled by five options (--dn, --mindiffs,
--mindiv, --minh, --xn). Sequences are first sorted by decreasing abundance (if available), and
compared on their plus strand only (case insensitive).

In de novo mode, input fasta file should present abundance annotations (pattern [;]size=integer[;]
in the fasta header). The input order influences the chimera detection, so we recommend to sort
sequences by decreasing abundance (default of --derep_fulllength command). If your sequence set
needs to be sorted, please see the --sortbysize command in the sorting section.

--abskew real
When using --uchime_denovo, the abundance skew is used to distinguish in a 3-way
alignment which sequence is the chimera and which are the parents. The assumption is that
chimeras appear later in the PCR amplification process and are therefore less abundant
than their parents. The default value is 2.0, which means that the parents should be at
least 2 times more abundant than their chimera. Any positive value greater than 1.0 can
be used.

--alignwidth positive integer
Width of the 3-way alignments in --uchimealns output. The default value is 80. Set to 0
to eliminate wrapping.

--chimeras filename
Output chimeric sequences to filename, in fasta format. Output order may vary when using
multiple threads.

--db filename
When using --uchime_ref, detect chimeras using the fasta-formatted reference sequences
contained in filename. Reference sequences are assumed to be chimera-free. Chimeras will
not be detected if their parents (or sufficiently close relatives) are not present in the
database.

--dn real
No vote pseudo-count (parameter n in the chimera scoring function) (default value is
1.4).

--mindiffs positive integer
Minimum number of differences per segment (default value is 3).

--mindiv real
Minimum divergence from closest parent (default value is 0.8).

--minh real
Minimum score (h). Increasing this value tends to reduce the number of false positives
and to decrease sensitivity. Default value is 0.28, and values ranging from 0.0 to 1.0
included are accepted.

--nonchimeras filename
Output non-chimeric sequences to filename, in fasta format. Output order may vary when
using multiple threads.

--self When using --uchime_ref, ignore a reference sequence when its label matches the label of
the query sequence (useful to estimate false-positive rate in reference sequences).

--selfid When using --uchime_ref, ignore a reference sequence when its nucleotide sequence is
strictly identical with the query sequence.

--threads positive integer
Number of computation threads to use (1 to 256) with --uchime_ref. The number of threads
should be lesser or equal to the number of available CPU cores. The default is to use all
available resources and to launch one thread per logical core.

--uchime_denovo filename
Detect chimeras present in the fasta-formatted filename, without external references
(i.e. de novo). Automatically sort the sequences in filename by decreasing abundance
beforehand (see the sorting section for details). Multithreading is not supported.

--uchime_ref filename
Detect chimeras present in the fasta-formatted filename by comparing them with reference
sequences (option --db). Multithreading is supported.

--uchimealns filename
Write the 3-way global alignments (parentA, parentB, chimera) to filename using a human-
readable format. Use --alignwidth to modify alignment length. Output order may vary when
using multiple threads.

--uchimeout filename
Write chimera detection results to filename using the uchime tab-separated format of 18
fields (see the list below). Use --uchimeout5 to use a format compatible with usearch v5
and earlier versions. Rows output order may vary when using multiple threads.

1. score: higher score means a more likely chimeric alignment.

2. Q: query sequence label.

3. A: parent A sequence label.

4. B: parent B sequence label.

5. T: top parent sequence label (i.e. parent most similar to the query). That
field is removed when using --uchimeout5.

6. idQM: percentage of similarity of query (Q) and model (M) constructed as a
part of parent A and a part of parent B.

7. idQA: percentage of similarity of query (Q) and parent A.

8. idQB: percentage of similarity of query (Q) and parent B.

9. idAB: percentage of similarity of parent A and parent B.

10. idQT: percentage of similarity of query (Q) and top parent (T).

11. LY: yes votes in the left part of the model.

12. LN: no votes in the left part of the model.

13. LA: abstain votes in the left part of the model.

14. RY: yes votes in the right part of the model.

15. RN: no votes in the right part of the model.

16. RA: abstain votes in the right part of the model.

17. div: divergence, defined as (idQM - idQT).

18. YN: query is chimeric (Y), or not (N), or is a borderline case (?).

--uchimeout5
When using --uchimeout, write chimera detection results using a tab-separated format of
17 fields (drop the 5th field of --uchimeout), compatible with usearch version 5 and
earlier versions.

--xn real
No vote weight (parameter beta in the scoring function) (default value is 8.0).

Clustering options:

vsearch implements a single-pass, greedy star-clustering algorithm, similar to the algorithms
implemented in usearch, DNAclust and sumaclust for example. Important parameters are the global
clustering threshold (--id) and the pairwise identity definition (--iddef).

--centroids filename
Output cluster centroid sequences to filename, in fasta format. The centroid is the
sequence that seeded the cluster (i.e. the first sequence of the cluster).

--cluster_fast filename
Clusterize the fasta sequences in filename, automatically perform a sorting by decreasing
sequence length beforehand.

--cluster_size filename
Clusterize the fasta sequences in filename, automatically perform a sorting by decreasing
sequence abundance beforehand.

--cluster_smallmem filename
Clusterize the fasta sequences in filename without automatically modifying their order
beforehand. Sequence are expected to be sorted by decreasing sequence length, unless
--usersort is used.

--clusters string
Output each cluster to a separate fasta file using the prefix string and a ticker (0, 1,
2, etc.) to construct the path and filenames.

--consout filename
Output cluster consensus sequences to filename. For each cluster, a multiple alignment is
computed, and a consensus sequence is constructed by taking the majority symbol
(nucleotide or gap) from each column of the alignment. Columns containing a majority of
gaps are skipped, except for terminal gaps.

--id real
Do not add the target to the cluster if the pairwise identity with the centroid is lower
than real (value ranging from 0.0 to 1.0 included). The pairwise identity is defined as
the number of (matching columns) / (alignment length - terminal gaps). That definition
can be modified by --iddef.

--iddef 0|1|2|3|4
Change the pairwise identity definition used in --id. Values accepted are:

0. CD-HIT definition: (matching columns) / (shortest sequence length).

1. edit distance: (matching columns) / (alignment length).

2. edit distance excluding terminal gaps (same as --id).

3. Marine Biological Lab definition counting each extended gap (internal or
terminal) as a single difference: 1.0 - [(mismatches + gaps)/(longest sequence
length)]

4. BLAST definition, equivalent to --iddef 2 in a context of global pairwise
alignment.

--msaout filename
Output a multiple sequence alignment and a consensus sequence for each cluster to
filename, in fasta format. The consensus sequence is constructed by taking the majority
symbol (nucleotide or gap) from each column of the alignment. Columns containing a
majority of gaps are skipped, except for terminal gaps.

--qmask none|dust|soft
Mask simple repeats and low-complexity regions in sequences using the dust or the soft
algorithms, or do not mask (none). Warning, when using soft masking, clustering becomes
case sensitive. The default is to mask using dust.

--sizein Take into account the abundance annotations present in the input fasta file (search for
the pattern "[>;]size=integer[;]" in sequence headers).

--sizeout
Add abundance annotations to the output fasta files (add the pattern ";size=integer;" to
sequence headers). If --sizein is specified, abundance annotations are reported to output
files, and each cluster centroid receives a new abundance value corresponding to the
total abundance of the amplicons included in the cluster (--centroids option). If
--sizein is not specified, input abundances are set to 1 for amplicons, and to the number
of amplicons per cluster for centroids.

--strand plus|both
When comparing sequences with the cluster seed, check the plus strand only (default) or
check both strands.

--threads positive integer
Number of computation threads to use (1 to 256). The number of threads should be lesser
or equal to the number of available CPU cores. The default is to use all available
resources and to launch one thread per logical core.

--uc filename
Output clustering results in filename using a uclust-like format. For a description of
the format, see <http://www.drive5.com/usearch/manual/ucout.html>.

--usersort
When using --cluster_smallmem, allow any sequence input order, not just a decreasing
length ordering.

Most searching options also apply to clustering:
--alnout, --blast6out, --fastapairs, --matched, --notmatched, --maxaccept, --maxreject,
--samout, --userout, --userfields, score filtering, gap penalties, masking. (see the
Searching section).

Dereplication options:

--derep_fulllength filename
Merge strictly identical sequences contained in filename. Identical sequences are defined
as having the same length and the same string of nucleotides (case insensitive, T and U
are considered the same).

--maxuniquesize positive integer
Discard sequences with an abundance value greater than integer.

--minuniquesize positive integer
Discard sequences with an abundance value smaller than integer.

--output filename
Write the dereplicated sequences to filename, in fasta format and sorted by decreasing
abundance. Identical sequences receive the header of the first sequence of their group.
If --sizeout is used, the number of occurrences (i.e. abundance) of each sequence is
indicated at the end of their fasta header using the pattern ";size=integer;".

--sizein Take into account the abundance annotations present in the input fasta file (search for
the pattern "[>;]size=integer[;]" in sequence headers).

--sizeout
Add abundance annotations to the output fasta file (add the pattern ";size=integer;" to
sequence headers). If --sizein is specified, each unique sequence receives a new
abundance value corresponding to its total abundance (sum of the abundances of its
occurrences). If --sizein is not specified, input abundances are set to 1, and each
unique sequence receives a new abundance value corresponding to its number of occurrences
in the input file.

--strand plus|both
When searching for strictly identical sequences, check the plus strand only (default) or
check both strands.

--topn positive integer
Output only the top integer sequences (i.e. the most abundant).

--uc filename
Output dereplication results in filename using a uclust-like format. For a description of
the format, see <http://www.drive5.com/usearch/manual/ucout.html>. In the context of
dereplication, the option --uc_allhits has no effect on the --uc output.

Masking options:

An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides are
silently set to uppercase before masking, unless the --qmask soft option is used. Here are the
results of combined masking options --qmask (or --dbmask for database sequences) and --hardmask,
assuming each input sequences contains both lower and uppercase nucleotides:

qmask hardmask action
───────────────────────────────────────────────────────────────────
none off no masking, all symbols uppercased
none on no masking, all symbols uppercased
dust off masked symbols lowercased, others uppercased
dust on masked symbols changed to Ns, others uppercased
soft off lowercase symbols masked, no case changes
soft on lowercase symbols masked and changed to Ns

--hardmask
Mask low-complexity regions by replacing them with Ns instead of setting them to lower
case.

--maskfasta filename
Mask simple repeats and low-complexity regions in sequences contained in filename. The
default is to mask using dust (use --qmask to modify that behavior).

--output filename
Write the masked sequences to filename, in fasta format.

--qmask none|dust|soft
Mask simple repeats and low-complexity regions in sequences using the dust or the soft
algorithms, or do not mask (none). The default is to mask using dust.

Pairwise alignment options:

The results of the n * (n - 1) / 2 pairwise alignments are written to the result files specified
with --alnout, --blast6out, --fastapairs --matched, --notmatched, --samout, --uc or --userout (see
Searching section below). Specify either the --acceptall option to output all pairwise alignments,
or specify an identity level with --id to discard weak alignments. Most other accept/reject
options (see Searching options below) may also be used. Sequences are aligned on their plus strand
only.

--acceptall
Write the results of all alignments to output files. This option overrides all other
accept/reject options (including --id).

--allpairs_global filename
Perform optimal global pairwise alignments of all vs. all fasta sequences contained in
filename. This command is multi-threaded.

--id real
Reject the sequence match if the pairwise identity is lower than real (value ranging from
0.0 to 1.0 included).

Searching options:

--alnout filename
Write pairwise global alignments to filename using a human-readable format. Use --rowlen
to modify alignment length. Output order may vary when using multiple threads.

--blast6out filename
Write search results to filename using a blast-like tab-separated format of twelve fields
(listed below), with one line per query-target matching (or lack of matching if
--output_no_hits is used). Output order may vary when using multiple threads. A similar
output can be obtain with --userout filename and --userfields
query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits. A complete list and
description is available in the section "Userfields" of this manual.

1. query: query label.

2. target: target (database sequence) label. The field is set to "*" if there is
no alignment.

3. id: percentage of identity (real value ranging from 0.0 to 100.0). The
percentage identity is defined as 100 * (matching columns) / (alignment length
- terminal gaps). See fields id0 to id4 for other definitions.

4. alnlen: length of the query-target alignment (number of columns). The field is
set to 0 if there is no alignment.

5. mism: number of mismatches in the alignment (zero or positive integer value).

6. opens: number of columns containing a gap opening (zero or positive integer
value).

7. qlo: first nucleotide of the query aligned with the target. Always equal to 1
if there is an alignment, 0 otherwise.

8. qhi: last nucleotide of the query aligned with the target. Always equal to the
length of the pairwise alignment. The field is set to 0 if there is no
alignment.

9. tlo: irst nucleotide of the target aligned with the query. Always equal to 1
if there is an alignment, 0 otherwise.

10. thi: last nucleotide of the target aligned with the query. Always equal to the
length of the pairwise alignment. The field is set to 0 if there is no
alignment.

11. evalue: expectancy-value (not computed for nucleotide alignments). Always set
to -1.

12. bits: bit score (not computed for nucleotide alignments). Always set to 0.

--db filename
Compare query sequences (specified with --usearch_global) to the fasta-formatted target
sequences contained in filename, using global pairwise alignment.

--dbmask none|dust|soft
Mask simple repeats and low-complexity regions in target database sequences using the
dust or the soft algorithms, or do not mask (none). Warning, when using soft masking
search commands become case sensitive. The default is to mask using dust.

--dbmatched filename
Write database target sequences matching at least one query sequence to filename, in
fasta format. If the option --sizeout is used, the number of queries that matched each
target sequence is indicated using the pattern ";size=integer;".

--dbnotmatched filename
Write database target sequences not matching query sequences to filename, in fasta
format.

--fastapairs filename
Write pairwise alignments of query and target sequences to filename, in fasta format.

--fulldp Dummy option for compatibility with usearch. To maximize search sensitivity, vsearch uses
a 8-way 16-bit SIMD vectorized full dynamic programming algorithm (Needleman-Wunsch),
whether or not --fulldp is specified.

--gapext string
Set penalties for a gap extension. See --gapopen for a complete description of the
penalty declaration system. The default is to initialize the six gap extending penalties
using a penalty of 2 for extending internal gaps and a penalty of 1 for extending
terminal gaps, in both query and target sequences (i.e. 2I/1E).

--gapopen string
Set penalties for a gap opening. A gap opening can occur in six different contexts: in
the query (Q) or in the target (T) sequence, at the left (L) or right (R) extremity of
the sequence, or inside the sequence (I). Sequence symbols (Q and T) can be combined with
location symbols (L, I, and R), and numerical values to declare penalties for all
possible contexts: aQL/bQI/cQR/dTL/eTI/fTR, where abcdef are zero or positive integers,
and "/" is used as a separator.
To simplify declarations, the location symbols (L, I, and R) can be combined, the symbol
(E) can be used to treat both extremities (L and R) equally, and the symbols Q and T can
be omitted to treat query and target sequences equally. For instance, the default is to
declare a penalty of 20 for opening internal gaps and a penalty of 2 for opening terminal
gaps (left or right), in both query and target sequences (i.e. 20I/2E). If only a
numerical value is given, without any sequence or location symbol, then the penalty
applies to all gap openings. To forbid gap-opening, an infinite penalty value can be
declared with the symbol "*". To use vsearch as a semi-global aligner, a null-penalty can
be applied to the left (L) or right (R) gaps.
vsearch always initializes the six gap opening penalties using the default parameters
(20I/2E). The user is then free to declare only the values he/she wants to modify. The
string is scanned from left to right, accepted symbols are (0123456789/LIREQT*), and
later values override previous values.
Please note that vsearch, in contrast to usearch, only allows integer gap penalties.
Because the lowest gap penalties are 0.5 by default in usearch, all default scores and
gap penalties in vsearch have been doubled to maintain equivalent penalties and to
produce identical alignments.

--hardmask
Mask low-complexity regions by replacing them with Ns instead of setting them to lower
case. For more information, please see the Masking section.

--id real
Reject the sequence match if the pairwise identity is lower than real (value ranging from
0.0 to 1.0 included). The search process sorts target sequences by decreasing number of
k-mers they have in common with the query sequence, using that information as a proxy for
sequence similarity. That efficient pre-filtering will also prevent pairwise alignments
with weakly matching targets, as there needs to be at least 6 shared k-mers to start the
pairwise alignment, and at least one out of every 16 k-mers from the query needs to match
the target. Consequently, using values lower than --id 0.5 is not likely to capture more
weakly matching targets. The pairwise identity is by default defined as the number of
(matching columns) / (alignment length - terminal gaps). That definition can be modified
by --iddef.

--iddef 0|1|2|3|4
Change the pairwise identity definition used in --id. Values accepted are:

0. CD-HIT definition: (matching columns) / (shortest sequence length).

1. edit distance: (matching columns) / (alignment length).

2. edit distance excluding terminal gaps (same as --id).

3. Marine Biological Lab definition counting each extended gap (internal or
terminal) as a single difference: 1.0 - [(mismatches + gaps)/(longest sequence
length)]

4. BLAST definition, equivalent to --iddef 2 in a context of global pairwise
alignment.

The option --userfields accepts the fields id0 to id4, in addition to the field id, to
report the pairwise identity values corresponding to the different definitions.

--idprefix positive integer
Reject the sequence match if the first integer nucleotides of the target do not match the
query.

--idsuffix positive integer
Reject the sequence match if the last integer nucleotides of the target do not match the
query.

--leftjust
Reject the sequence match if the pairwise alignment begins with gaps.

--match integer
Score assigned to a match (i.e. identical nucleotides) in the pairwise alignment. The
default value is 2.

--matched filename
Write query sequences matching database target sequences to filename, in fasta format.

--maxaccepts positive integer
Maximum number of hits to accept before stopping the search. The default value is 1. This
option works in pair with --maxrejects. The search process sorts target sequences by
decreasing number of k-mers they have in common with the query sequence, using that
information as a proxy for sequence similarity. After pairwise alignments, if the first
target sequence passes the acceptation criteria, it is accepted as best hit and the
search process stops for that query. If --maxaccepts is set to a higher value, more hits
are accepted. If --maxaccepts and --maxrejects are both set to 0, the complete database
is searched.

--maxdiffs positive integer
Reject the sequence match if the alignment contains at least integer substitutions,
insertions or deletions.

--maxgaps positive integer
Reject the sequence match if the alignment contains at least integer insertions or
deletions.

--maxhits positive integer
Maximum number of hits to show once the search is terminated (hits are sorted by
decreasing identity). Unlimited by default. That option applies to --alnout, --blast6out,
--fastapairs, --samout, --uc, or --userout output files.

--maxid real
Reject the sequence match if the percentage of identity between the two sequences is
greater than real.

--maxqsize positive integer
Reject query sequences with an abundance greater than integer.

--maxqt real
Reject if the query/target sequence length ratio is greater than real.

--maxrejects positive integer
Maximum number of non-matching target sequences to consider before stopping the search.
The default value is 32. This option works in pair with --maxaccepts. The search process
sorts target sequences by decreasing number of k-mers they have in common with the query
sequence, using that information as a proxy for sequence similarity. After pairwise
alignments, if none of the first 32 examined target sequences pass the acceptation
criteria, the search process stops for that query (no hit). If --maxrejects is set to a
higher value, more target sequences are considered. If --maxaccepts and --maxrejects are
both set to 0, the complete database is searched.

--maxsizeratio real
Reject if the query/target abundance ratio is greater than real.

--maxsl real
Reject if the shorter/longer sequence length ratio is greater than real.

--maxsubs positive integer
Reject the sequence match if the pairwise alignment contains more than integer
substitutions.

--mid real
Reject the sequence match if the percentage of identity is lower than real (ignoring all
gaps, internal and terminal).

--mincols positive integer
Reject the sequence match if the alignment length is shorter than integer.

--minqt real
Reject if the query/target sequence length ratio is lower than real.

--minsizeratio real
Reject if the query/target abundance ratio is lower than real.

--minsl real
Reject if the shorter/longer sequence length ratio is lower than real.

--mintsize positive integer
Reject target sequences with an abundance lower than integer.

--mismatch integer
Score assigned to a mismatch (i.e. different nucleotides) in the pairwise alignment. The
default value is -4.

--notmatched filename
Write query sequences not matching database target sequences to filename, in fasta
format.

--output_no_hits
Write both matching and non-matching queries to --alnout, --blast6out, --samout or
--userout output files (--uc and --uc_allhits output files always feature non-matching
queries). Non-matching queries are labelled "No hits" in --alnout files.

--qmask none|dust|soft
Mask simple repeats and low-complexity regions in query sequences using the dust or the
soft algorithms, or do not mask (none). Warning, when using soft masking search commands
become case sensitive. The default is to mask using dust.

--query_cov real
Reject if the fraction of the query aligned to the target sequence is lower than real.
The query coverage is computed as (matches + mismatches) / query sequence length.
Internal or terminal gaps are not taken into account.

--rightjust
Reject the sequence match if the pairwise alignment ends with gaps.

--rowlen positive integer
Width of alignment lines in --alnout output. The default value is 64. Set to 0 to
eliminate wrapping.

--samout filename
Write alignment results to filename in the SAM format. For a description of the format,
see <https://github.com/samtools/hts-specs>. Output order may vary when using multiple
threads.

--self Reject the sequence match if the query and target labels are identical.

--selfid Reject the sequence match if the query and target sequences are strictly identical.

--sizeout
Add abundance annotations to the output of the option --dbmatched (using the pattern
";size=integer;"), to report the number of queries that matched each target.

--strand plus|both
When searching for similar sequences, check the plus strand only (default) or check both
strands.

--target_cov real
Reject the sequence match if the fraction of the target sequence aligned to the query
sequence is lower than real. The target coverage is computed as (matches + mismatches) /
target sequence length. Internal or terminal gaps are not taken into account.

--top_hits_only
Output only the hits with the highest percentage of identity with the query.

--uc filename
Output searching results in filename using a uclust-like format. For a description of the
format, see <http://www.drive5.com/usearch/manual/ucout.html>. Output order may vary when
using multiple threads.

--uc_allhits
When using the --uc option, show all hits, not just the top hit for each query.

--usearch_global filename
Compare target sequences (--db) to the fasta-formatted query sequences contained in
filename, using global pairwise alignment.

--userfields string
When using --userout, select and order the fields written to the output file. Fields are
separated by "+" (e.g. query+target+id). See the "Userfields" section for a complete list
of fields.

--userout filename
Write user-defined tab-separated output to filename. Select the fields with the option
--userfields. Output order may vary when using multiple threads. If --userfields is empty
or not present, filename is empty.

--weak_id real
Show hits with percentage of identity of at least real, without terminating the search. A
normal search stops as soon as enough hits are found (as defined by --maxaccepts,
--maxrejects, and --id). As --weak_id reports weak hits that are not deduced from
--maxaccepts, high --id values can be used, hence preserving both speed and sensitivity.
Logically, real must be smaller than the value indicated by --id.

--wordlength positive integer
Length of words (i.e. k-mers) for database indexing. The range of possible values goes
from 3 to 15, but values near 8 are generally recommended. Longer words may reduce the
sensitivity for weak similarities, but can increase accuracy. On the other hand, shorter
words may increase sensitivity, but can reduce accuracy. Computation time will generally
increase with shorter words and decrease with longer words. Memory requirements for a
part of the index increase with a factor of 4 each time word length increases by one
nucleotide, and this generally becomes significant for long words (12 or more). The
default value is 8.

Shuffling options:

--output filename
Write the shuffled sequences to filename, in fasta format.

--seed positive integer
When shuffling sequence order, use integer as seed. A given seed will always produce the
same output order (useful for replicability). Set to 0 to use a pseudo-random seed
(default behavior).

--shuffle filename
Pseudo-randomly shuffle the order of sequences contained in filename.

--topn positive integer
Output only the top integer sequences.

Sorting options:
Fasta entries are sorted by decreasing abundance (--sortbysize) or sequence length
(--sortbylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and
label increasing alpha-numerical order (--sortbylength), or just by label increasing alpha-
numerical order (--sortbysize). Label sorting assumes that all sequences have unique labels. The
same applies to the automatic sorting performed during chimera checking (--uchime_denovo),
dereplication (--derep_fulllength), and clustering (--cluster_fast and --cluster_size).

--maxsize positive integer
When using --sortbysize, discard sequences with an abundance value greater than integer.

--minsize positive integer
When using --sortbysize, discard sequences with an abundance value smaller than integer.

--output filename
Write the sorted sequences to filename, in fasta format.

--relabel string
Relabel sequence using the prefix string and a ticker (1, 2, 3, etc.) to construct the
new headers. Use --sizeout to conserve the abundance annotations.

--sizeout
When using --relabel, report abundance annotations to the output fasta file (using the
pattern ";size=integer;").

--sortbylength filename
Sort by decreasing length the sequences contained in filename. See the general options
--minseqlength and --maxseqlength to eliminate short and long sequences.

--sortbysize filename
Sort by decreasing abundance the sequences contained in filename (the pattern
"[>;]size=integer[;]" has to be present). See the options --minsize and --maxsize to
eliminate rare and dominant sequences.

--topn positive integer
Output only the top integer sequences (i.e. the longest or the most abundant).

Userfields (fields accepted by the --userfields option):

aln Print a string of M (match), D (delete, i.e. a gap in the query) and I (insert, i.e. a
gap in the target) representing the pairwise alignment. Empty field if there is no
alignment.

alnlen Print the length of the query-target alignment (number of columns). The field is set to 0
if there is no alignment.

bits Bit score (not computed for nucleotide alignments). Always set to 0.

caln Compact representation of the pairwise alignment using the CIGAR format (Compact
Idiosyncratic Gapped Alignment Report): M (match), D (deletion) and I (insertion). Empty
field if there is no alignment.

evalue E-value (not computed for nucleotide alignments). Always set to -1.

exts Number of columns containing a gap extension (zero or positive integer value).

gaps Number of columns containing a gap (zero or positive integer value).

id Percentage of identity (real value ranging from 0.0 to 100.0). The percentage identity is
defined as 100 * (matching columns) / (alignment length - terminal gaps).

id0 CD-HIT definition of the percentage of identity (real value ranging from 0.0 to 100.0)
using the length of the shortest sequence in the pairwise alignment as denominator: 100 *
(matching columns) / (shortest sequence length).

id1 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit
distance: 100 * (matching columns) / (alignment length).

id2 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit
distance, excluding terminal gaps. The field id2 is an alias for the field id.

id3 Marine Biological Lab definition of the percentage of identity (real value ranging from
0.0 to 100.0), counting each extended gap (internal or terminal) as a single difference
and using the length of the longest sequence in the pairwise alignment as denominator:
100 * (1.0 - [(mismatches + gaps) / (longest sequence length)]).

id4 BLAST definition of the percentage of identity (real value ranging from 0.0 to 100.0),
equivalent to --iddef 2 in a context of global pairwise alignment.

ids Number of matches in the alignment (zero or positive integer value).

mism Number of mismatches in the alignment (zero or positive integer value).

opens Number of columns containing a gap opening (zero or positive integer value).

pairs Number of columns containing only nucleotides. That value corresponds to the length of
the alignment minus the gap-containing columns (zero or positive integer value).

pctgaps Number of columns containing gaps expressed as a percentage of the alignment length (real
value ranging from 0.0 to 100.0).

pctpv Percentage of positive columns. When working with nucleotide sequences, this is
equivalent to the percentage of matches (real value ranging from 0.0 to 100.0).

pv Number of positive columns. When working with nucleotide sequences, this is equivalent to
the number of matches (zero or positive integer value).

qcov Fraction of the query sequence that is aligned with the target sequence (real value
ranging from 0.0 to 100.0). The query coverage is computed as 100.0 * (matches +
mismatches) / query sequence length. Internal or terminal gaps are not taken into
account. The field is set to 0.0 if there is no alignment.

qframe Query frame (-3 to +3). That field only concerns coding sequences and is not computed by
vsearch. Always set to +0.

qhi Last nucleotide of the query aligned with the target. Always equal to the length of the
pairwise alignment. The field is set to 0 if there is no alignment.

qihi Last nucleotide of the query aligned with the target (ignoring terminal gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.

qilo First nucleotide of the query aligned with the target (ignoring initial gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.

ql Query sequence length (positive integer value). The field is set to 0 if there is no
alignment.

qlo First nucleotide of the query aligned with the target. Always equal to 1 if there is an
alignment, 0 otherwise.

qrow Print the sequence of the query segment as seen in the pairwise alignment (i.e. with gap
insertions if need be). Empty field if there is no alignment.

qs Query segment length. Always equal to query sequence length.

qstrand Query strand orientation (+ or - for nucleotide sequences). Empty field if there is no
alignment.

query Query label.

raw Raw alignment score (negative, null or positive integer value). The score is the sum of
match rewards minus mismatch penalties, gap openings and gap extensions. The field is set
to 0 if there is no alignment.

target Target label. The field is set to "*" if there is no alignment.

tcov Fraction of the target sequence that is aligned with the query sequence (real value
ranging from 0.0 to 100.0). The target coverage is computed as 100.0 * (matches +
mismatches) / target sequence length. Internal or terminal gaps are not taken into
account. The field is set to 0.0 if there is no alignment.

tframe Target frame (-3 to +3). That field only concerns coding sequences and is not computed by
vsearch. Always set to +0.

thi Last nucleotide of the target aligned with the query. Always equal to the length of the
pairwise alignment. The field is set to 0 if there is no alignment.

tihi Last nucleotide of the target aligned with the query (ignoring terminal gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.

tilo First nucleotide of the target aligned with the query (ignoring initial gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.

tl Target sequence length (positive integer value). The field is set to 0 if there is no
alignment.

tlo First nucleotide of the target aligned with the query. Always equal to 1 if there is an
alignment, 0 otherwise.

trow Print the sequence of the target segment as seen in the pairwise alignment (i.e. with gap
insertions if need be). Empty field if there is no alignment.

ts Target segment length. Always equal to target sequence length. The field is set to 0 if
there is no alignment.

tstrand Target strand orientation (+ or - for nucleotide sequences). Always set to "+", so
reverse strand matches have tstrand "+" and qstrand "-". Empty field if there is no
alignment.

DELIBERATE CHANGES

If you are a usearch user, our objective is to make you feel at home. That's why vsearch was designed to
behave like usearch, to some extent. Like any complex software, usearch is not free from quirks and
inconsistencies. We decided not to reproduce some of them, and for complete transparency, to document
here the deliberate changes we made.

During a search with usearch, when using the options --blast6out and --output_no_hits, for queries with
no match the number of fields reported is 13, where it should be 12. This is corrected in vsearch.

The field raw of the --userfields option is not informative in usearch. This is corrected in vsearch.

The fields qlo, qhi, tlo, thi now have counterparts (qilo, qihi, tilo, tihi) reporting alignment
coordinates ignoring terminal gaps.

In usearch, when using the option --output_no_hits, queries that receive no match are reported in
blast6out file, but not in the alignment output file. This is corrected in vsearch.

vsearch introduces a new --cluster_size command that sorts sequences by decreasing abundance before
clustering.

vsearch reintroduces --iddef alternative pairwise identity definitions that were removed from usearch.

vsearch extends the --topn option to sorting commands.

vsearch extends the --sizein option to dereplication (--derep_fulllength) and clustering
(--cluster_fast).

vsearch treats T and U as identical nucleotides during dereplication.

vsearch sorting is stabilized by using sequence abundances or sequences labels as secondary or tertiary
keys.

NOVELTIES

       vsearch introduces new options not present in usearch 7. They are described in the "Options"  section  of
       this manual. Here is a short list:

       - alignwidth (chimera checking)

       - cluster_size (clustering)

       - fasta_width (general option)

       - iddef (clustering, pairwise alignment, searching)

       - maxuniquesize (dereplication)

       - shuffle (shuffling)

EXAMPLES

       Align all sequences in a database with each other and output all pairwise alignments:

              vsearch --allpairs_global database.fas --alnout results.aln --acceptall

       Check  for  the  presence  of chimeras (de novo); parents should be at least 1.5 times more abundant than
       chimeras. Output non-chimeric sequences in fasta format (no wrapping):

              vsearch --uchime_denovo queries.fas --nonchimeras results.fas --fasta_width 0 --abskew 1.5

       Cluster with a 97% similarity threshold, collect cluster centroids, and write cluster descriptions  using
       a uclust-like format:

              vsearch --cluster_fast queries.fas --id 0.97 --centroids centroids.fas --uc clusters.uc

       Dereplicate  the  sequences contained in queries.fas, take into account the abundance information already
       present, write unwrapped sequences to output with the new abundance information,  discard  all  sequences
       with an abundance of 1:

              vsearch    --derep_fulllength   queries.fas   --output   queries_masked.fas   --sizein   --sizeout
              --fasta_width 0 --minuniquesize 2

       Mask simple repeats and low complexity regions in the input fasta file (masked regions  are  lowercased),
       and write the results to the output file:

              vsearch --maskfasta queries.fas --output queries_masked.fas --qmask dust

       Search  queries in a reference database, with a 80%-similarity threshold, take terminal gaps into account
       when calculating pairwise similarities:

              vsearch --usearch_global queries.fas --db references.fas --alnout results.aln --id 0.8 --iddef 1

       Search a sequence dataset against itself (ignore self hits), get all matches with at least 60%  identity,
       and collect results in a blast-like tab-separated format:

              vsearch  --usearch_global  queries.fas --db queries.fas --id 0.6 --self --blast6out results.blast6
              --maxaccepts 0 --maxrejects 0

       Shuffle the input fasta file (change the order of sequences) in a repeatable fashion  (fixed  seed),  and
       write unwrapped fasta sequences to the output file:

              vsearch --shuffle queries.fas --output queries_shuffled.fas --seed 13 --fasta_width 0

       Sort   by  decreasing  abundance  the  sequences  contained  in  queries.fas  (using  the  "size=integer"
       information), relabel the sequences while preserving the abundance  information  (with  --sizeout),  keep
       only sequences with an abundance equal to or greater than 2:

              vsearch   --sortbysize   queries.fas  --output  queries_sorted.fas  --relabel  sampleA_  --sizeout
              --minsize 2

AUTHORS

       Implementation by Torbjørn Rognes and Tomás Flouri, documentation by Frédéric Mahé.

REPORTING BUGS

       Submit suggestions and bug-reports at <https://github.com/torognes/vsearch/issues>, send a  pull  request
       on  <https://github.com/torognes/vsearch>, or compose a friendly or curmudgeont e-mail to Torbjørn Rognes
       <torognes@ifi.uio.no>.

AVAILABILITY

       Source code and binaries are available at <https://github.com/torognes/vsearch>.

COPYRIGHT

       Copyright (C) 2014, 2015 Torbjørn Rognes, Frédéric Mahé and Tomás Flouri.

       This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero
       General Public License as published by the Free Software Foundation, either version 3 of the License,  or
       any later version.

       This  program  is  distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
       the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU  Affero  General
       Public License for more details.

       You  should  have  received  a copy of the GNU Affero General Public License along with this program.  If
       not, see <http://www.gnu.org/licenses/>.

       vsearch includes code from Google's CityHash project by Geoff Pike and Jyrki Alakuijala,  providing  some
       excellent hash functions available under a MIT license.

       vsearch includes code derived from Tatusov and Lipman's DUST program that is in the public domain.

       vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark Adler.

       vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.

VERSION HISTORY

New features and important modifications of vsearch (short lived or minor bug releases may not be
mentioned):

v1.0.0 released November 28th, 2014
First public release.

v1.0.1 released December 1st, 2014
Bug fixes (sortbysize, semicolon after size annotation in headers) and minor changes
(labels as secondary sort key for most sorts, treat T and U as identical for dereplication,
only output size in dbmatched file if sizeout specified).

v1.0.2 released December 6th, 2014
Bug fixes (ssse3/sse4.1 requirement, memory leak).

v1.0.3 released December 6th, 2014
Bug fix (now writes help to stdout instead of stderr).

v1.0.4 released December 8th, 2014
Added --allpairs_global option. Reduced memory requirements slightly. Removed memory leaks.

v1.0.5 released December 9th, 2014
Fixes a minor bug with --allpairs_global and --acceptall options.

v1.0.6 released December 14th, 2014
Fixes a memory allocation bug in chimera detection (--uchime_ref option).

v1.0.7 released December 19th, 2014
Fixes a bug in the output from chimera detection with the --uchimeout option.

v1.0.8 released January 22nd, 2015
Introduces several changes and bug fixes:

- a new linear memory aligner for alignment of sequences longer than 5,000 nucleotides,

- a new --cluster_size command that sorts sequences by decreasing abundance before
clustering,

- meaning of userfields qlo, qhi, tlo, thi changed for compatibility with usearch,

- new userfields qilo, qihi, tilo, tihi gives alignment coordinates ignoring terminal gaps,

- in --uc output files, a perfect alignment is indicated with a "=" sign,

- the option --cluster_fast will now sort sequences by decreasing length, then by
decreasing abundance and finally by sequence identifier,

- default --maxseqlength value set to 50,000 nucleotides,

- fix for bug in alignment in rare cases,

- fix for lack of detection of under- or overflow in SIMD aligner.

v1.0.9 released January 22nd, 2015
Fixes a bug in the function sorting sequences by decreasing abundance (--sortbysize).

v1.0.10 released January 23rd, 2015
Fixes a bug where the sizein option was ignored and always treated as on, affecting
clustering and dereplication commands.

v1.0.11 released February 5th, 2015
Introduces the possibility to output results in SAM format (for clustering, pairwise
alignment and searching).

v1.0.12 released February 6th, 2015
Temporarily fixes a problem with long headers in FASTA files.

v1.0.13 released February 17th, 2015
Fix a memory allocation problem when computing multiple sequence alignments with the
--msaout and --consout options, as well as a memory leak. Also increased line buffer for
reading FASTA files to 4MB.

v1.0.14 released February 17th, 2015
Fix a bug where the multiple alignment and consensus sequence computed after clustering
ignored the strand of the sequences. Also decreased size of line buffer for reading FASTA
files to 1MB again due to excessive stack memory usage.

v1.0.15 released February 18th, 2015
Fix bug in calculation of identity metric between sequences when using the MBL definition
(--iddef 3).

v1.0.16 released February 19th, 2015
Integrated patches from Debian for increased compatibility with various architectures.

v1.1.0 released February 20th, 2015
Added the --quiet option to suppress all output to stdout and stdout except for warnings
and fatal errors. Added the --log option to write messages to a log file.

v1.1.1 released February 20th, 2015
Added info about --log and --quiet options to help text.

v1.1.2 released March 18th, 2015
Fix bug with large datasets. Fix format of help info.

v1.1.3 released March 18th, 2015
Fix more bugs with large datasets.

version 1.1.3 March 18, 2015 vsearch(1)