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NAME
uchime - reads a fasta file and reference file and outputs potentially chimeric sequences
DESCRIPTION
The chimera.uchime command reads a fasta file and reference file and outputs potentially
chimeric sequences. The original uchime program was written by Robert C. Edgar.
SYNOPSIS
uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime]
[--uchimealns results.alns]
OPTIONS
--input filename
Query sequences in FASTA format. If the --db option is not specificed, uchime uses
de novo detection. In de novo mode, relative abundance must be given by a string
/ab=xxx/ somewhere in the label, where xxx is a floating-point number, e.g.
>F00QGH67HG/ab=1.2/.
--db filename
Reference database in FASTA format. Optional, if not specified uchime uses de novo
mode.
***WARNING*** The database is searched ONLY on the plus strand. You MUST include
reverse-complemented sequences in the database if you want both strands to be
searched.
--abskew x
Minimum abundance skew. Default 1.9. De novo mode only. Abundance skew is:
min [ abund(parent1), abund(parent2) ] / abund(query).
--uchimeout filename
Output in tabbed format with one record per query sequence. First field is score
(h), second field is query label. For details, see manual.
--uchimealns filename
Multiple alignments of query sequences to parents in humanreadable format.
Alignments show columns with differences that support or contradict a chimeric
model.
--minh h
Minimum score to report chimera. Default 0.3. Values from 0.1 to 5 might be
reasonable. Lower values increase sensitivity but may report more false positives.
If you decrease --xn, you may need to increase --minh, and vice versa.
--mindiv div
Minimum divergence ratio, default 0.5. Div ratio is 100% - %identity between query
sequence and the closest candidate for being a parent. If you don't care about very
close chimeras, then you could increase --mindiv to, say, 1.0 or 2.0, and also
decrease --min h, say to 0.1, to increase sensitivity. How well this works will
depend on your data. Best is to tune parameters on a good benchmark.
--xn beta
Weight of a no vote, also called the beta parameter. Default 8.0. Decreasing this
weight to around 3 or 4 may give better performance on denoised data.
--dn n
Pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to
change this unless you can retune to a good benchmark for your data. Reasonable
values are probably in the range from 0.2 to 2.
--xa w
Weight of an abstain vote. Default 1. So far, results do not seem to be very
sensitive to this parameter, but if you have a good training set might be worth
trying. Reasonable values might range from 0.1 to 2.
--chunks n
Number of chunks to extract from the query sequence when searching for parents.
Default 4.
--[no]ovchunks
[Do not] use overlapping chunks. Default do not.
--minchunk n
Minimum length of a chunk. Default 64.
--idsmoothwindow w
Length of id smoothing window. Default 32.
--minsmoothid f
Minimum factional identity over smoothed window of candidate parent. Default 0.95.
--maxp n
Maximum number of candidate parents to consider. Default 2. In tests so far,
increasing --maxp gives only a very small improvement in sensivity but tends to
increase the error rate quite a bit.
--[no]skipgaps --[no]skipgaps2
These options control how gapped columns affect counting of diffs. If --skipgaps
is specified, columns containing gaps do not found as diffs. If --skipgaps2 is
specified, if column is immediately adjacent to a column containing a gap, it is
not counted as a diff. Default is --skipgaps --skipgaps2.
--minlen L --maxlen L
Minimum and maximum sequence length. Defaults 10, 10000. Applies to both query and
reference sequences.
--ucl
Use local-X alignments. Default is global-X. On tests so far, global-X is always
better; this option is retained because it just might work well on some future type
of data.
--queryfract f
Minimum fraction of the query sequence that must be covered by a local-X alignment.
Default 0.5. Applies only when --ucl is specified.
--quiet
Do not display progress messages on stderr.
--log filename
Write miscellaneous information to the log file. Mostly of interest to me (the
algorithm developer). Use --verbose to get more info.
--self
In reference database mode, exclude a reference sequence if it has the same label
as the query. This is useful for benchmarking by using the ref db as a query to
test for false positives.
--abskew <float>
help
--absort <str>
help
--abx <float>
help
--allpairs <str>
help
--alpha <str>
help
--band <uint>
help
--blast6out <str>
help
--[no]blast_termgaps
help
--blastout <str>
help
--bump <uint>
help
--[no]cartoon_orfs
help
--cc <str>
help
--chain_evalue <float>
help
--chain_targetfract <float>
help
--chainhits <str>
help
--chainout <str>
help
--chunks <uint>
help
--clstr2uc <str>
help
--clump <str>
help
--clump2fasta <str>
help
--clumpfasta <str>
help
--clumpout <str>
help
--cluster <str>
help
--compilerinfo
Write info about compiler types and #defines to stdout.
--computekl <str>
help
--db <str>
help
--dbstep <uint>
help
--[no]denovo
help
--derep
help
--diffchar <str>
help
--dn <float>
help
--doug <str>
help
--droppct <uint>
help
--evalue <float>
help
--evalue_g <float>
help
--exact
help
--[no]fastalign
help
--fastapairs <str>
help
--fastq2fasta <str>
help
--findorfs <str>
help
--[no]flushuc
help
--frame <int>
help
--fspenalty <float>
help
--gapext <str>
help
--gapopen <str>
help
--getseqs <str>
help
--global
help
--hash help
--hashsize <uint>
help
--help Display command-line options.
--hireout <str>
help
--hspalpha <str>
help
--id <float>
help
--idchar <str>
help
--iddef <uint>
help
--idprefix <uint>
help
--ids <str>
help
--idsmoothwindow <uint>
help
--idsuffix <uint>
help
--indexstats <str>
help
--input <str>
help
--[no]isort
help
--k <uint>
help
--ka_dbsize <float>
help
--ka_gapped_k <float>
help
--ka_gapped_lambda <float>
help
--ka_ungapped_k <float>
help
--ka_ungapped_lambda <float>
help
--[no]label_ab
help
--labels <str>
help
--[no]leftjust
help
--lext <float>
help
--local
help
--log <str>
Log file name.
--[no]log_hothits
help
--[no]log_query
help
--[no]logmemgrows
help
--logopts
Log options.
--[no]logwordstats
help
--lopen <float>
help
--makeindex <str>
help
--match <float>
help
--matrix <str>
help
--max2 <uint>
help
--maxaccepts <uint>
help
--maxclump <uint>
help
--maxlen <uint>
help
--maxovd <uint>
help
--maxp <uint>
help
--maxpoly <uint>
help
--maxqgap <uint>
help
--maxrejects <uint>
help
--maxspan1 <uint>
help
--maxspan2 <uint>
help
--maxtargets <uint>
help
--maxtgap <uint>
help
--mcc <str>
help
--mergeclumps <str>
help
--mergesort <str>
help
--minchunk <uint>
help
--mincodons <uint>
help
--mindiffs <uint>
help
--mindiv <float>
help
--minh <float>
help
--minhsp <uint>
help
--minlen <uint>
help
--minorfcov <uint>
help
--minspanratio1 <float>
help
--minspanratio2 <float>
help
--[no]minus_frames
help
--mismatch <float>
help
--mkctest <str>
help
--[no]nb
help
--optimal
help
--orfstyle <uint>
help
--otusort <str>
help
--output <str>
help
--[no]output_rejects
help
--probmx <str>
help
--query <str>
help
--queryfract <float>
help
--querylen <uint>
help
--quiet
Turn off progress messages.
--randseed <uint>
help
--realign
help
--[no]rev
help
--[no]rightjust
help
--rowlen <uint>
help
--secs <uint>
help
--seeds <str>
help
--seedsout <str>
help
--seedt1 <float>
help
--seedt2 <float>
help
--self help
--[no]selfid
help
--simcl <str>
help
--[no]skipgaps
help
--[no]skipgaps2
help
--sort <str>
help
--sortuc <str>
help
--sparsedist <str>
help
--sparsedistparams <str>
help
--split <float>
help
--[no]ssort
help
--sspenalty <float>
help
--[no]stable_sort
help
--staralign <str>
help
--stepwords <uint>
help
--strand <str>
help
--targetfract <float>
help
--targetlen <uint>
help
--tmpdir <str>
help
--[no]trace
help
--tracestate <str>
help
--[no]trunclabels
help
--[no]twohit
help
--uc <str>
help
--uc2clstr <str>
help
--uc2fasta <str>
help
--uc2fastax <str>
help
--uchime <str>
help
--uchimealns <str>
help
--uchimeout <str>
help
--[no]ucl
help
--uhire <str>
help
--ungapped
help
--userfields <str>
help
--userout <str>
help
--usersort
help
--uslink <str>
help
--[no]usort
help
--utax <str>
help
--[no]verbose
help
--version
Show version and exit.
--w <uint>
help
--weak_evalue <float>
help
--weak_id <float>
help
--[no]wordcountreject
help
--[no]wordweight
help
--xa <float>
help
--xdrop_g <float>
help
--xdrop_nw <float>
help
--xdrop_u <float>
help
--xdrop_ug <float>
help
--xframe <str>
help
--xlat help
--xn <float>
help
AUTHOR
Robert C. Edgar
SEE ALSO
http://www.drive5.com/uchime