Provided by: swarm_2.2.2+dfsg-1_amd64 
NAME
swarm — find clusters of nearly-identical nucleotide amplicons
SYNOPSIS
swarm [ options ] filename
DESCRIPTION
Environmental or clinical molecular studies generate large volumes of amplicons (e.g., 16S or 18S SSU-
rRNA sequences) that need to be clustered into molecular operational taxonomic units (OTUs). Common
clustering methods are based on greedy, input-order dependent algorithms, with arbitrary selection of
global cluster size and cluster centroids. To address that problem, we developed swarm, a fast and robust
method that recursively groups amplicons with d or less differences (i.e. substitutions, insertions or
deletions). swarm produces natural and stable clusters centered on local peaks of abundance, mostly free
from input-order dependency induced by centroid selection.
Exact clustering is impractical on large data sets when using a naïve all-vs-all approach (more precisely
a 2-combination without repetitions), as it implies unrealistic numbers of pairwise comparisons. swarm is
based on a maximum number of differences d between two amplicons, and focuses only on very close local
relationships. For d = 1, the default value, swarm uses an algorithm of linear complexity that generates
all possible single mutations and performs exact-string matching by comparing hash-values. For d = 2 or
greater, swarm uses an algorithm of quadratic complexity that performs pairwise string comparisons. An
efficient k-mer-based filtering and an astute use of comparisons results obtained during the clustering
process allows swarm to avoid most of the amplicon comparisons needed in a naïve approach. To speed up
the remaining amplicon comparisons, swarm implements an extremely fast Needleman-Wunsch algorithm making
use of the Streaming SIMD Extensions (SSE2) of modern x86-64 CPUs. If SSE2 instructions are not
available, swarm exits with an error message.
swarm can read nucleotide amplicons in fasta format from a normal file or from the standard input (using
a pipe or a redirection). The amplicon identifier is defined as the string comprised between the '>'
symbol and the first space or the end of the line, whichever comes first. As swarm outputs lists of
amplicon identifiers, amplicon identifiers must be unique to avoid ambiguity; swarm exits with an error
message if identifiers are not unique. Amplicon identifiers must end with a '_' followed by a positive
integer representing the amplicon copy number (or abundance annotation; usearch/vsearch users can use the
option -z to use the ';size=' annotation). Abundance annotations play a crucial role in the clustering
process, and swarm exits with an error message if that information is not available. The amplicon
sequence is defined as a string of [ACGT] or [ACGU] symbols (case insensitive, 'U' is replaced with 'T'
internally), starting after the end of the identifier line and ending before the next identifier line or
the file end; swarm silently removes newline symbols ('\n' or '\r') and exits with an error message if
any other symbol is present.
General options
-h, --help
display this help and exit successfully.
-t, --threads positive integer
number of computation threads to use. Values between 1 and 256 are accepted, but we recommend to
use a number of threads lesser or equal to the number of available CPU cores. Default number of
threads is 1.
-v, --version
output version information and exit successfully.
-- delimit the option list. Later arguments, if any, are treated as operands even if they begin
with '-'. For example, 'swarm -- -file.fasta' reads from the file '-file.fasta'.
Clustering options
-d, --differences zero or positive integer
maximum number of differences allowed between two amplicons, meaning that two amplicons will be
grouped if they have integer (or less) differences. This is swarm's most important parameter.
The number of differences is calculated as the number of mismatches (substitutions, insertions
or deletions) between the two amplicons once the optimal pairwise global alignment has been
found (see 'pairwise alignment advanced options' to influence that step). Any integer from 0 to
255 can be used, but high d values will decrease the taxonomical resolution of swarm results.
Commonly used d values are 1, 2 or 3, rarely higher. When using d = 0, swarm will output results
corresponding to a strict dereplication of the dataset, i.e. merging identical amplicons.
Warning, whatever the d value, swarm requires fasta entries to present abundance values. Default
number of differences d is 1.
-n, --no-otu-breaking
deactivate the built-in OTU refinement (not recommended). Amplicon abundance values are used to
identify transitions among in-contact OTUs and to separate them, yielding higher-resolution
clustering results. That option prevents that separation, and in practice, allows the creation
of a link between amplicons A and B, even if the abundance of B is higher than the abundance of
A.
Fastidious options
-b, --boundary positive integer
when using the option --fastidious (-f), define the minimum mass of a large OTU. By default, an
OTU with a mass of 3 or more is considered large. Conversely, an OTU is small if it has a mass
of less than 3, meaning that it is composed of either one amplicon of abundance 2, or two
amplicons of abundance 1. Any positive value greater than 1 can be specified. Using higher
boundary values will speed up the second pass, but also reduce the taxonomical resolution of
swarm results. Default mass of a large OTU is 3.
-c, --ceiling positive integer
when using the option --fastidious (-f), define swarm's maximum memory footprint (in megabytes).
swarm will adjust the --bloom-bits (-y) value of the Bloom filter to fit within the specified
amount of memory. The value must be at least 3.
-f, --fastidious
when working with d = 1, perform a second clustering pass to reduce the number of small OTUs
(recommended option). During the first clustering pass, an intermediate amplicon can be missing
for purely stochastic reasons, interrupting the aggregation process. The fastidious option will
create virtual amplicons, allowing to graft small OTUs upon bigger ones. By default, an OTU is
small if it has a mass of 2 or less (see the --boundary option to modify that value). To speed
things up, swarm uses a Bloom filter to store intermediate results. Warning, the second
clustering pass can be 2 to 3 times slower than the first pass and requires much more memory to
store the virtual amplicons in Bloom filters. See the options --bloom-bits (-y) or --ceiling
(-c) to control the memory footprint of the Bloom filter. The fastidious option modifies
clustering results: the output files produced by the options --log (-l), --output-file (-o),
--mothur (-r), --uclust-file, and --seeds (-w) are updated to reflect these modifications; the
file --statistics-file (-s) is partially updated (columns 6 and 7 are not updated); the output
file --internal-structure (-i) is partially updated (column 5 is not updated for amplicons that
belonged to the small OTU).
-y, --bloom-bits positive integer
when using the option --fastidious (-f), define the size (in bits) of each entry in the Bloom
filter. That option allows to balance the efficiency (i.e. speed) and the memory footprint of
the Bloom filter. Large values will make the Bloom filter more efficient but will require more
memory. Any value between 2 and 64 can be used. Default value is 16. See the --ceiling (-c)
option for an alternative way to control the memory footprint.
Input/output options
-a, --append-abundance positive integer
set abundance value to use when some or all amplicons in the input file lack abundance values
(_integer, or ;size=integer; when using -z). Warning, it is not recommended to use swarm on
datasets where abundance values are all identical. We provide that option as a courtesy to
advanced users, please use it carefully. swarm exits with an error message if abundance values
are missing and if this option is not used.
-i, --internal-structure filename
output all pairs of nearly-identical amplicons to filename using a five-columns tab-delimited
format:
1. amplicon A label.
2. amplicon B label.
3. number of differences between amplicons A and B (positive integer).
4. OTU number (positive integer). OTUs are numbered in their order of delineation,
starting from 1. All pairs of amplicons belonging to the same OTU will receive the
same number.
5. cummulated number of steps from the OTU seed to amplicon B (positive integer). When
using the option --fastidious (-f), the actual number of steps between grafted
amplicons and the OTU seed cannot be re-computed efficiently and is always set to 2
for the amplicon pair linking the small OTU to the big OTU. Cummulated number of
steps in the small OTU (if any) are left unchanged.
-l, --log filename
output all messages to filename instead of standard error, with the exception of error messages
of course. That option is useful in situations where writing to standard error is problematic
(for example, with certain job schedulers).
-o, --output-file filename
output clustering results to filename. Results consist of a list of OTUs, one OTU per line. An
OTU is a list of amplicon identifiers separated by spaces. That output format can be modified by
the option --mothur (-r). Default is to write to standard output.
-r, --mothur
output clustering results in a format compatible with Mothur. That option modifies swarm's
default output format.
-s, --statistics-file filename
output statistics to filename. The file is a tab-separated table with one OTU per row and seven
columns of information:
1. number of unique amplicons in the OTU,
2. total abundance of amplicons in the OTU,
3. identifier of the initial seed,
4. initial seed abundance,
5. number of amplicons with an abundance of 1 in the OTU,
6. maximum number of iterations before the OTU reached its natural limit,
7. cummulated number of steps along the path joining the seed and the furthermost
amplicon in the OTU. Please note that the actual number of differences between the
seed and the furthermost amplicon is usually much smaller. When using the option
--fastidious (-f), grafted amplicons are not taken into account.
-u, --uclust-file filename
output clustering results in filename using a tab-separated uclust-like format with 10 columns
and 3 different type of entries (S, H or C). That option does not modify swarm's default output
format. Each fasta sequence in the input file can be either a cluster centroid (S) or a hit (H)
assigned to a cluster. Cluster records (C) summarize information (size, centroid label) for each
cluster. Column content varies with the type of entry (S, H or C):
1. Record type: S, H, or C.
2. Cluster number (zero-based).
3. Centroid length (S), query length (H), or cluster size (C).
4. Percentage of similarity with the centroid sequence (H), or set to '*' (S, C).
5. Match orientation + or - (H), or set to '*' (S, C).
6. Not used, always set to '*' (S, C) or to zero (H).
7. Not used, always set to '*' (S, C) or to zero (H).
8. set to '*' (S, C) or, for H, compact representation of the pairwise alignment using
the CIGAR format (Compact Idiosyncratic Gapped Alignment Report): M (match), D
(deletion) and I (insertion). The equal sign '=' indicates that the query is
identical to the centroid sequence.
9. Label of the query sequence (H), or of the centroid sequence (S, C).
10. Label of the centroid sequence (H), or set to '*' (S, C).
-w, --seeds filename
output OTU representatives to filename in fasta format. The abundance value of each OTU
representative is the sum of the abundances of all the amplicons in the OTU.
-z, --usearch-abundance
accept amplicon abundance values in usearch/vsearch's style (>label;size=integer[;]). That
option influences the abundance annotation style used in output files.
Pairwise alignment advanced options
when using d > 1, swarm recognizes advanced command-line options modifying the pairwise global alignment
scoring parameters:
-m, --match-reward positive integer
Default reward for a nucleotide match is 5.
-p, --mismatch-penalty positive integer
Default penalty for a nucleotide mismatch is 4.
-g, --gap-opening-penalty positive integer
Default gap opening penalty is 12.
-e, --gap-extension-penalty positive integer
Default gap extension penalty is 4.
As swarm focuses on close relationships (e.g., d = 2 or 3), clustering results are resilient to pairwise
alignment model parameters modifications. When clustering using a higher d value, modifying model
parameters has a stronger impact.
EXAMPLES
Clusterize the data set myfile.fasta into OTUs with the finest resolution possible (1 difference, built-
in breaking, fastidious option) using 4 computation threads. OTUs are written to the file myfile.swarms,
and OTU representatives are written to myfile.representatives.fasta.
swarm -t 4 -f -w myfile.representatives.fasta < myfile.fasta > myfile.swarms
AUTHORS
Concept by Frédéric Mahé, implementation by Torbjørn Rognes.
CITATION
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014) Swarm: robust and fast clustering method for
amplicon-based studies. PeerJ 2:e593 <https://doi.org/10.7717/peerj.593>
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2015) Swarm v2: highly-scalable and high-resolution
amplicon clustering. PeerJ 3:e1420 <https://doi.org/10.7717/peerj.1420>
REPORTING BUGS
Submit suggestions and bug-reports at <https://github.com/torognes/swarm/issues>, send a pull request on
<https://github.com/torognes/swarm>, or compose a friendly or curmudgeonly e-mail to Frédéric Mahé
<mahe@rhrk.uni-kl.de> and Torbjørn Rognes <torognes@ifi.uio.no>.
AVAILABILITY
Source code and binaries are available at <https://github.com/torognes/swarm>
COPYRIGHT
Copyright (C) 2012-2017 Frédéric Mahé & Torbjørn Rognes
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/>.
SEE ALSO
swipe, an extremely fast Smith-Waterman database search tool by Torbjørn Rognes (available from
<https://github.com/torognes/swipe>).
vsearch, an open-source re-implementation of the classic uclust clustering method (by Robert C. Edgar),
along with other amplicon filtering and searching tools. vsearch is implemented by Torbjørn Rognes and
documented by Frédéric Mahé, and is available at <https://github.com/torognes/vsearch>.
VERSION HISTORY
New features and important modifications of swarm (short lived or minor bug releases are not mentioned):
v2.2.2 released December 12, 2017
Version 2.2.2 fixes a bug that would cause Swarm to wait forever in very rare cases when
multiple threads were used.
v2.2.1 released October 27, 2017
Version 2.2.1 fixes a memory allocation bug for d = 1 and duplicated sequences.
v2.2.0 released October 17, 2017
Version 2.2.0 fixes several problems and improves usability. Corrected output to structure
and uclust files when using fastidious mode. Corrected abundance output in some cases.
Added check for duplicated sequences and fixed check for duplicated sequence IDs. Checks
for empty sequences. Sorts sequences by additional fields to improve stability. Improves
compatibility with compilers and operating systems. Outputs sequences in upper case.
Allows 64-bit abundances. Shows message when waiting for input from stdin. Improves error
messages and warnings. Improves checking of command line options. Fixes remaining errors
reported by test suite. Updates documentation.
v2.1.13 released March 8, 2017
Version 2.1.13 removes a bug with the progress bar when writing seeds.
v2.1.12 released January 16, 2017
Version 2.1.12 removes a debugging message.
v2.1.11 released January 16, 2017
Version 2.1.11 fixes two bugs related to the SIMD implementation of alignment that might
result in incorrect alignments and scores. The bug only applies when d > 1.
v2.1.10 released December 22, 2016
Version 2.1.10 fixes two bugs related to gap penalties of alignments. The first bug may
lead to wrong aligments and similarity percentages reported in UCLUST (.uc) files. The
second bug makes Swarm use a slightly higher gap extension penalty than specified. The
default gap extension penalty used have actually been 4.5 instead of 4.
v2.1.9 released July 6, 2016
Version 2.1.9 fixes errors when compiling with GCC version 6.
v2.1.8 released March 11, 2016
Version 2.1.8 fixes a rare bug triggered when clustering extremely short undereplicated
sequences. Also, alignment parameters are not shown when d = 1.
v2.1.7 released February 24, 2016
Version 2.1.7 fixes a bug in the output of seeds with the -w option when d > 1 that was not
properly fixed in version 2.1.6. It also handles ascii character #13 (CR) in FASTA files
better. Swarm will now exit with status 0 if the -h or the -v option is specified. The help
text and some error messages have been improved.
v2.1.6 released December 14, 2015
Version 2.1.6 fixes problems with older compilers that do not have the x86intrin.h header
file. It also fixes a bug in the output of seeds with the -w option when d > 1.
v2.1.5 released September 8, 2015
Version 2.1.5 fixes minor bugs.
v2.1.4 released September 4, 2015
Version 2.1.4 fixes minor bugs in the swarm algorithm used for d = 1.
v2.1.3 released August 28, 2015
Version 2.1.3 adds checks of numeric option arguments.
v2.1.1 released March 31, 2015
Version 2.1.1 fixes a bug with the fastidious option that caused it to ignore some
connections between large and small OTUs.
v2.1.0 released March 24, 2015
Version 2.1.0 marks the first official release of swarm v2.
v2.0.7 released March 18, 2015
Version 2.0.7 writes abundance information in usearch style when using options -w (--seeds)
in combination with -z (--usearch-abundance).
v2.0.6 released March 13, 2015
Version 2.0.6 fixes a minor bug.
v2.0.5 released March 13, 2015
Version 2.0.5 improves the implementation of the fastidious option and adds options to
control memory usage of the Bloom filter (-y and -c). In addition, an option (-w) allows
to output OTU representatives sequences with updated abundances (sum of all abundances
inside each OTU). This version also enables swarm to run with d = 0.
v2.0.4 released March 6, 2015
Version 2.0.4 includes a fully parallelised implementation of the fastidious option.
v2.0.3 released March 4, 2015
Version 2.0.3 includes a working implementation of the fastidious option, but only the
initial clustering is parallelized.
v2.0.2 released February 26, 2015
Version 2.0.2 fixes SSSE3 problems.
v2.0.1 released February 26, 2015
Version 2.0.1 is a development version that contains a partial implementation of the
fastidious option, but it is not usable yet.
v2.0.0 released December 3, 2014
Version 2.0.0 is faster and easier to use, providing new output options
(--internal-structure and --log), new control options (--boundary, --fastidious,
--no-otu-breaking), and built-in OTU refinement (no need to use the python script anymore).
When using default parameters, a novel and considerably faster algorithmic approach is
used, guaranteeing swarm's scalability.
v1.2.21 released February 26, 2015
Version 1.2.21 is supposed to fix some problems related to the use of the SSSE3 CPU
instructions which are not always available.
v1.2.20 released November 6, 2014
Version 1.2.20 presents a production-ready version of the alternative algorithm (option
-a), with optional built-in OTU breaking (option -n). That alternative algorithmic approach
(usable only with d = 1) is considerably faster than currently used clustering algorithms,
and can deal with datasets of 100 million unique amplicons or more in a few hours. Of
course, results are rigourously identical to the results previously produced with swarm.
That release also introduces new options to control swarm output (options -i and -l).
v1.2.19 released October 3, 2014
Version 1.2.19 fixes a problem related to abundance information when the sequence
identifier includes multiple underscore characters.
v1.2.18 released September 29, 2014
Version 1.2.18 reenables the possibility of reading sequences from stdin if no file name is
specified on the command line. It also fixes a bug related to CPU features detection.
v1.2.17 released September 28, 2014
Version 1.2.17 fixes a memory allocation bug introduced in version 1.2.15.
v1.2.16 released September 27, 2014
Version 1.2.16 fixes a bug in the abundance sort introduced in version 1.2.15.
v1.2.15 released September 27, 2014
Version 1.2.15 sorts the input sequences in order of decreasing abundance unless they are
detected to be sorted already. When using the alternative algorithm for d = 1 it also sorts
all subseeds in order of decreasing abundance.
v1.2.14 released September 27, 2014
Version 1.2.14 fixes a bug in the output with the --swarm_breaker option (-b) when using
the alternative algorithm (-a).
v1.2.12 released August 18, 2014
Version 1.2.12 introduces an option --alternative-algorithm to use an extremely fast,
experimental clustering algorithm for the special case d = 1. Multithreading scalability of
the default algorithm has been noticeably improved.
v1.2.10 released August 8, 2014
Version 1.2.10 allows amplicon abundances to be specified using the usearch style in the
sequence header (e.g. '>id;size=1') when the -z option is chosen.
v1.2.8 released August 5, 2014
Version 1.2.8 fixes an error with the gap extension penalty. Previous versions used a gap
penalty twice as large as intended. That bug correction induces small changes in clustering
results.
v1.2.6 released May 23, 2014
Version 1.2.6 introduces an option --mothur to output clustering results in a format
compatible with the microbial ecology community analysis software suite Mothur
(<http://www.mothur.org/>).
v1.2.5 released April 11, 2014
Version 1.2.5 removes the need for a POPCNT hardware instruction to be present. swarm now
automatically checks whether POPCNT is available and uses a slightly slower software
implementation if not. Only basic SSE2 instructions are now required to run swarm.
v1.2.4 released January 30, 2014
Version 1.2.4 introduces an option --break-swarms to output all pairs of amplicons with d
differences to standard error. That option is used by the companion script
`swarm_breaker.py` to refine swarm results. The syntax of the inline assembly code is
changed for compatibility with more compilers.
v1.2 released May 16, 2013
Version 1.2 greatly improves speed by using alignment-free comparisons of amplicons based
on k-mer word content. For each amplicon, the presence-absence of all possible 5-mers is
computed and recorded in a 1024-bits vector. Vector comparisons are extremely fast and
drastically reduce the number of costly pairwise alignments performed by swarm. While
remaining exact, swarm 1.2 can be more than 100-times faster than swarm 1.1, when using a
single thread with a large set of sequences. The minor version 1.1.1, published just
before, adds compatibility with Apple computers, and corrects an issue in the pairwise
global alignment step that could lead to sub-optimal alignments.
v1.1 released February 26, 2013
Version 1.1 introduces two new important options: the possibility to output clustering
results using the uclust output format, and the possibility to output detailed statistics
on each OTU. swarm 1.1 is also faster: new filterings based on pairwise amplicon sequence
lengths and composition comparisons reduce the number of pairwise alignments needed and
speed up the clustering.
v1.0 released November 10, 2012
First public release.