uchime - Online in the Cloud

PROGRAM:

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

Mininum 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

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