.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH UCHIME "1" "July 2013" "uchime v4.2.40" "User Commands"
.SH NAME
uchime \- reads a fasta file and reference file and outputs potentially chimeric sequences
.SH 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.
.SH SYNOPSIS
.B uchime
\fB\-\-input\fR query.fasta [\-\-db db.fasta] [\-\-uchimeout results.uchime]
.IP
[\-\-uchimealns results.alns]
.SH OPTIONS
.PP
\fB\-\-input\fR filename
.IP
Query sequences in FASTA format.
If the \fB\-\-db\fR 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/.
.PP
\fB\-\-db\fR filename
.IP
Reference database in FASTA format.
Optional, if not specified uchime uses de novo mode.
.IP
***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.
.PP
\fB\-\-abskew\fR x
.IP
Minimum abundance skew. Default 1.9. De novo mode only.
Abundance skew is:
.IP
min [ abund(parent1), abund(parent2) ] / abund(query).
.PP
\fB\-\-uchimeout\fR filename
.IP
Output in tabbed format with one record per query sequence.
First field is score (h), second field is query label.
For details, see manual.
.PP
\fB\-\-uchimealns\fR filename
.IP
Multiple alignments of query sequences to parents in humanreadable format. Alignments show columns with differences
that support or contradict a chimeric model.
.PP
\fB\-\-minh\fR h
.IP
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 \fB\-\-xn\fR,
you may need to increase \fB\-\-minh\fR, and vice versa.
.PP
\fB\-\-mindiv\fR div
.IP
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 \fB\-\-mindiv\fR to, say, 1.0 or 2.0, and
also decrease \fB\-\-min\fR 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.
.PP
\fB\-\-xn\fR beta
.IP
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.
.PP
\fB\-\-dn\fR n
.IP
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.
.PP
\fB\-\-xa\fR w
.IP
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.
.PP
\fB\-\-chunks\fR n
.IP
Number of chunks to extract from the query sequence when searching
for parents. Default 4.
.PP
\fB\-\-[no]ovchunks\fR
.IP
[Do not] use overlapping chunks. Default do not.
.PP
\fB\-\-minchunk\fR n
.IP
Minimum length of a chunk. Default 64.
.PP
\fB\-\-idsmoothwindow\fR w
.IP
Length of id smoothing window. Default 32.
.PP
\fB\-\-minsmoothid\fR f
.IP
Minimum factional identity over smoothed window of candidate parent.
Default 0.95.
.PP
\fB\-\-maxp\fR n
.IP
Maximum number of candidate parents to consider. Default 2. In tests so
far, increasing \fB\-\-maxp\fR gives only a very small improvement in sensivity
but tends to increase the error rate quite a bit.
.PP
\fB\-\-[no]skipgaps\fR
\fB\-\-[no]skipgaps2\fR
.IP
These options control how gapped columns affect counting of diffs.
If \fB\-\-skipgaps\fR is specified, columns containing gaps do not found as diffs.
If \fB\-\-skipgaps2\fR is specified, if column is immediately adjacent to
a column containing a gap, it is not counted as a diff.
Default is \fB\-\-skipgaps\fR \fB\-\-skipgaps2\fR.
.PP
\fB\-\-minlen\fR L
\fB\-\-maxlen\fR L
.IP
Minimum and maximum sequence length. Defaults 10, 10000.
Applies to both query and reference sequences.
.PP
\fB\-\-ucl\fR
.IP
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.
.PP
\fB\-\-queryfract\fR f
.IP
Minimum fraction of the query sequence that must be covered by a local\-X
alignment. Default 0.5. Applies only when \fB\-\-ucl\fR is specified.
.PP
\fB\-\-quiet\fR
.IP
Do not display progress messages on stderr.
.PP
\fB\-\-log\fR filename
.IP
Write miscellaneous information to the log file. Mostly of interest
to me (the algorithm developer). Use \fB\-\-verbose\fR to get more info.
.PP
\fB\-\-self\fR
.IP
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.
.TP
\fB\-\-abskew\fR <float>
help
.TP
\fB\-\-absort\fR <str>
help
.TP
\fB\-\-abx\fR <float>
help
.TP
\fB\-\-allpairs\fR <str>
help
.TP
\fB\-\-alpha\fR <str>
help
.TP
\fB\-\-band\fR <uint>
help
.TP
\fB\-\-blast6out\fR <str>
help
.TP
\fB\-\-[no]blast_termgaps\fR
help
.TP
\fB\-\-blastout\fR <str>
help
.TP
\fB\-\-bump\fR <uint>
help
.TP
\fB\-\-[no]cartoon_orfs\fR
help
.TP
\fB\-\-cc\fR <str>
help
.TP
\fB\-\-chain_evalue\fR <float>
help
.TP
\fB\-\-chain_targetfract\fR <float>
help
.TP
\fB\-\-chainhits\fR <str>
help
.TP
\fB\-\-chainout\fR <str>
help
.TP
\fB\-\-chunks\fR <uint>
help
.TP
\fB\-\-clstr2uc\fR <str>
help
.TP
\fB\-\-clump\fR <str>
help
.TP
\fB\-\-clump2fasta\fR <str>
help
.TP
\fB\-\-clumpfasta\fR <str>
help
.TP
\fB\-\-clumpout\fR <str>
help
.TP
\fB\-\-cluster\fR <str>
help
.TP
\fB\-\-compilerinfo\fR
Write info about compiler types and #defines to stdout.
.TP
\fB\-\-computekl\fR <str>
help
.TP
\fB\-\-db\fR <str>
help
.TP
\fB\-\-dbstep\fR <uint>
help
.TP
\fB\-\-[no]denovo\fR
help
.TP
\fB\-\-derep\fR
help
.TP
\fB\-\-diffchar\fR <str>
help
.TP
\fB\-\-dn\fR <float>
help
.TP
\fB\-\-doug\fR <str>
help
.TP
\fB\-\-droppct\fR <uint>
help
.TP
\fB\-\-evalue\fR <float>
help
.TP
\fB\-\-evalue_g\fR <float>
help
.TP
\fB\-\-exact\fR
help
.TP
\fB\-\-[no]fastalign\fR
help
.TP
\fB\-\-fastapairs\fR <str>
help
.TP
\fB\-\-fastq2fasta\fR <str>
help
.TP
\fB\-\-findorfs\fR <str>
help
.TP
\fB\-\-[no]flushuc\fR
help
.TP
\fB\-\-frame\fR <int>
help
.TP
\fB\-\-fspenalty\fR <float>
help
.TP
\fB\-\-gapext\fR <str>
help
.TP
\fB\-\-gapopen\fR <str>
help
.TP
\fB\-\-getseqs\fR <str>
help
.TP
\fB\-\-global\fR
help
.TP
\fB\-\-hash\fR
help
.TP
\fB\-\-hashsize\fR <uint>
help
.TP
\fB\-\-help\fR
Display command\-line options.
.TP
\fB\-\-hireout\fR <str>
help
.TP
\fB\-\-hspalpha\fR <str>
help
.TP
\fB\-\-id\fR <float>
help
.TP
\fB\-\-idchar\fR <str>
help
.TP
\fB\-\-iddef\fR <uint>
help
.TP
\fB\-\-idprefix\fR <uint>
help
.TP
\fB\-\-ids\fR <str>
help
.TP
\fB\-\-idsmoothwindow\fR <uint>
help
.TP
\fB\-\-idsuffix\fR <uint>
help
.TP
\fB\-\-indexstats\fR <str>
help
.TP
\fB\-\-input\fR <str>
help
.TP
\fB\-\-[no]isort\fR
help
.TP
\fB\-\-k\fR <uint>
help
.TP
\fB\-\-ka_dbsize\fR <float>
help
.TP
\fB\-\-ka_gapped_k\fR <float>
help
.TP
\fB\-\-ka_gapped_lambda\fR <float>
help
.TP
\fB\-\-ka_ungapped_k\fR <float>
help
.TP
\fB\-\-ka_ungapped_lambda\fR <float>
help
.TP
\fB\-\-[no]label_ab\fR
help
.TP
\fB\-\-labels\fR <str>
help
.TP
\fB\-\-[no]leftjust\fR
help
.TP
\fB\-\-lext\fR <float>
help
.TP
\fB\-\-local\fR
help
.TP
\fB\-\-log\fR <str>
Log file name.
.TP
\fB\-\-[no]log_hothits\fR
help
.TP
\fB\-\-[no]log_query\fR
help
.TP
\fB\-\-[no]logmemgrows\fR
help
.TP
\fB\-\-logopts\fR
Log options.
.TP
\fB\-\-[no]logwordstats\fR
help
.TP
\fB\-\-lopen\fR <float>
help
.TP
\fB\-\-makeindex\fR <str>
help
.TP
\fB\-\-match\fR <float>
help
.TP
\fB\-\-matrix\fR <str>
help
.TP
\fB\-\-max2\fR <uint>
help
.TP
\fB\-\-maxaccepts\fR <uint>
help
.TP
\fB\-\-maxclump\fR <uint>
help
.TP
\fB\-\-maxlen\fR <uint>
help
.TP
\fB\-\-maxovd\fR <uint>
help
.TP
\fB\-\-maxp\fR <uint>
help
.TP
\fB\-\-maxpoly\fR <uint>
help
.TP
\fB\-\-maxqgap\fR <uint>
help
.TP
\fB\-\-maxrejects\fR <uint>
help
.TP
\fB\-\-maxspan1\fR <uint>
help
.TP
\fB\-\-maxspan2\fR <uint>
help
.TP
\fB\-\-maxtargets\fR <uint>
help
.TP
\fB\-\-maxtgap\fR <uint>
help
.TP
\fB\-\-mcc\fR <str>
help
.TP
\fB\-\-mergeclumps\fR <str>
help
.TP
\fB\-\-mergesort\fR <str>
help
.TP
\fB\-\-minchunk\fR <uint>
help
.TP
\fB\-\-mincodons\fR <uint>
help
.TP
\fB\-\-mindiffs\fR <uint>
help
.TP
\fB\-\-mindiv\fR <float>
help
.TP
\fB\-\-minh\fR <float>
help
.TP
\fB\-\-minhsp\fR <uint>
help
.TP
\fB\-\-minlen\fR <uint>
help
.TP
\fB\-\-minorfcov\fR <uint>
help
.TP
\fB\-\-minspanratio1\fR <float>
help
.TP
\fB\-\-minspanratio2\fR <float>
help
.TP
\fB\-\-[no]minus_frames\fR
help
.TP
\fB\-\-mismatch\fR <float>
help
.TP
\fB\-\-mkctest\fR <str>
help
.TP
\fB\-\-[no]nb\fR
help
.TP
\fB\-\-optimal\fR
help
.TP
\fB\-\-orfstyle\fR <uint>
help
.TP
\fB\-\-otusort\fR <str>
help
.TP
\fB\-\-output\fR <str>
help
.TP
\fB\-\-[no]output_rejects\fR
help
.TP
\fB\-\-probmx\fR <str>
help
.TP
\fB\-\-query\fR <str>
help
.TP
\fB\-\-queryfract\fR <float>
help
.TP
\fB\-\-querylen\fR <uint>
help
.TP
\fB\-\-quiet\fR
Turn off progress messages.
.TP
\fB\-\-randseed\fR <uint>
help
.TP
\fB\-\-realign\fR
help
.TP
\fB\-\-[no]rev\fR
help
.TP
\fB\-\-[no]rightjust\fR
help
.TP
\fB\-\-rowlen\fR <uint>
help
.TP
\fB\-\-secs\fR <uint>
help
.TP
\fB\-\-seeds\fR <str>
help
.TP
\fB\-\-seedsout\fR <str>
help
.TP
\fB\-\-seedt1\fR <float>
help
.TP
\fB\-\-seedt2\fR <float>
help
.TP
\fB\-\-self\fR
help
.TP
\fB\-\-[no]selfid\fR
help
.TP
\fB\-\-simcl\fR <str>
help
.TP
\fB\-\-[no]skipgaps\fR
help
.TP
\fB\-\-[no]skipgaps2\fR
help
.TP
\fB\-\-sort\fR <str>
help
.TP
\fB\-\-sortuc\fR <str>
help
.TP
\fB\-\-sparsedist\fR <str>
help
.TP
\fB\-\-sparsedistparams\fR <str>
help
.TP
\fB\-\-split\fR <float>
help
.TP
\fB\-\-[no]ssort\fR
help
.TP
\fB\-\-sspenalty\fR <float>
help
.TP
\fB\-\-[no]stable_sort\fR
help
.TP
\fB\-\-staralign\fR <str>
help
.TP
\fB\-\-stepwords\fR <uint>
help
.TP
\fB\-\-strand\fR <str>
help
.TP
\fB\-\-targetfract\fR <float>
help
.TP
\fB\-\-targetlen\fR <uint>
help
.TP
\fB\-\-tmpdir\fR <str>
help
.TP
\fB\-\-[no]trace\fR
help
.TP
\fB\-\-tracestate\fR <str>
help
.TP
\fB\-\-[no]trunclabels\fR
help
.TP
\fB\-\-[no]twohit\fR
help
.TP
\fB\-\-uc\fR <str>
help
.TP
\fB\-\-uc2clstr\fR <str>
help
.TP
\fB\-\-uc2fasta\fR <str>
help
.TP
\fB\-\-uc2fastax\fR <str>
help
.TP
\fB\-\-uchime\fR <str>
help
.TP
\fB\-\-uchimealns\fR <str>
help
.TP
\fB\-\-uchimeout\fR <str>
help
.TP
\fB\-\-[no]ucl\fR
help
.TP
\fB\-\-uhire\fR <str>
help
.TP
\fB\-\-ungapped\fR
help
.TP
\fB\-\-userfields\fR <str>
help
.TP
\fB\-\-userout\fR <str>
help
.TP
\fB\-\-usersort\fR
help
.TP
\fB\-\-uslink\fR <str>
help
.TP
\fB\-\-[no]usort\fR
help
.TP
\fB\-\-utax\fR <str>
help
.TP
\fB\-\-[no]verbose\fR
help
.TP
\fB\-\-version\fR
Show version and exit.
.TP
\fB\-\-w\fR <uint>
help
.TP
\fB\-\-weak_evalue\fR <float>
help
.TP
\fB\-\-weak_id\fR <float>
help
.TP
\fB\-\-[no]wordcountreject\fR
help
.TP
\fB\-\-[no]wordweight\fR
help
.TP
\fB\-\-xa\fR <float>
help
.TP
\fB\-\-xdrop_g\fR <float>
help
.TP
\fB\-\-xdrop_nw\fR <float>
help
.TP
\fB\-\-xdrop_u\fR <float>
help
.TP
\fB\-\-xdrop_ug\fR <float>
help
.TP
\fB\-\-xframe\fR <str>
help
.TP
\fB\-\-xlat\fR
help
.TP
\fB\-\-xn\fR <float>
help
.SH AUTHOR
Robert C. Edgar
.SH SEE ALSO
http://www.drive5.com/uchime