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UCHIME(1) User Commands UCHIME(1)

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.
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--[no]blast_termgaps
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--[no]cartoon_orfs
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Write info about compiler types and #defines to stdout.
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--[no]denovo
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--[no]fastalign
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--[no]flushuc
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Display command-line options.
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--[no]isort
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--[no]label_ab
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--[no]leftjust
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Log file name.
--[no]log_hothits
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--[no]log_query
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--[no]logmemgrows
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Log options.
--[no]logwordstats
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--[no]minus_frames
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--[no]nb
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--[no]output_rejects
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Turn off progress messages.
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--[no]rev
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--[no]rightjust
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--[no]selfid
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--[no]skipgaps
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--[no]skipgaps2
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--[no]ssort
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--[no]stable_sort
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--[no]trace
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--[no]trunclabels
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--[no]twohit
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--[no]ucl
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--[no]usort
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--[no]verbose
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Show version and exit.
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--[no]wordcountreject
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--[no]wordweight
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AUTHOR

Robert C. Edgar

SEE ALSO

http://www.drive5.com/uchime

July 2013 uchime v4.2.40