--- name: "uchime" section: "1" platform: "linux" package: "mothur" version: "1.48.1-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/uchime" --- # uchime(1) reads a fasta file and reference file and outputs potentially chimeric sequences ## 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** \ help - **--absort** \ help - **--abx** \ help - **--allpairs** \ help - **--alpha** \ help - **--band** \ help - **--blast6out** \ help - **--\[no\]blast\_termgaps** help - **--blastout** \ help - **--bump** \ help - **--\[no\]cartoon\_orfs** help - **--cc** \ help - **--chain\_evalue** \ help - **--chain\_targetfract** \ help - **--chainhits** \ help - **--chainout** \ help - **--chunks** \ help - **--clstr2uc** \ help - **--clump** \ help - **--clump2fasta** \ help - **--clumpfasta** \ help - **--clumpout** \ help - **--cluster** \ help - **--compilerinfo** Write info about compiler types and #defines to stdout. - **--computekl** \ help - **--db** \ help - **--dbstep** \ help - **--\[no\]denovo** help - **--derep** help - **--diffchar** \ help - **--dn** \ help - **--doug** \ help - **--droppct** \ help - **--evalue** \ help - **--evalue\_g** \ help - **--exact** help - **--\[no\]fastalign** help - **--fastapairs** \ help - **--fastq2fasta** \ help - **--findorfs** \ help - **--\[no\]flushuc** help - **--frame** \ help - **--fspenalty** \ help - **--gapext** \ help - **--gapopen** \ help - **--getseqs** \ help - **--global** help - **--hash** help - **--hashsize** \ help - **--help** Display command-line options. - **--hireout** \ help - **--hspalpha** \ help - **--id** \ help - **--idchar** \ help - **--iddef** \ help - **--idprefix** \ help - **--ids** \ help - **--idsmoothwindow** \ help - **--idsuffix** \ help - **--indexstats** \ help - **--input** \ help - **--\[no\]isort** help - **--k** \ help - **--ka\_dbsize** \ help - **--ka\_gapped\_k** \ help - **--ka\_gapped\_lambda** \ help - **--ka\_ungapped\_k** \ help - **--ka\_ungapped\_lambda** \ help - **--\[no\]label\_ab** help - **--labels** \ help - **--\[no\]leftjust** help - **--lext** \ help - **--local** help - **--log** \ Log file name. - **--\[no\]log\_hothits** help - **--\[no\]log\_query** help - **--\[no\]logmemgrows** help - **--logopts** Log options. - **--\[no\]logwordstats** help - **--lopen** \ help - **--makeindex** \ help - **--match** \ help - **--matrix** \ help - **--max2** \ help - **--maxaccepts** \ help - **--maxclump** \ help - **--maxlen** \ help - **--maxovd** \ help - **--maxp** \ help - **--maxpoly** \ help - **--maxqgap** \ help - **--maxrejects** \ help - **--maxspan1** \ help - **--maxspan2** \ help - **--maxtargets** \ help - **--maxtgap** \ help - **--mcc** \ help - **--mergeclumps** \ help - **--mergesort** \ help - **--minchunk** \ help - **--mincodons** \ help - **--mindiffs** \ help - **--mindiv** \ help - **--minh** \ help - **--minhsp** \ help - **--minlen** \ help - **--minorfcov** \ help - **--minspanratio1** \ help - **--minspanratio2** \ help - **--\[no\]minus\_frames** help - **--mismatch** \ help - **--mkctest** \ help - **--\[no\]nb** help - **--optimal** help - **--orfstyle** \ help - **--otusort** \ help - **--output** \ help - **--\[no\]output\_rejects** help - **--probmx** \ help - **--query** \ help - **--queryfract** \ help - **--querylen** \ help - **--quiet** Turn off progress messages. - **--randseed** \ help - **--realign** help - **--\[no\]rev** help - **--\[no\]rightjust** help - **--rowlen** \ help - **--secs** \ help - **--seeds** \ help - **--seedsout** \ help - **--seedt1** \ help - **--seedt2** \ help - **--self** help - **--\[no\]selfid** help - **--simcl** \ help - **--\[no\]skipgaps** help - **--\[no\]skipgaps2** help - **--sort** \ help - **--sortuc** \ help - **--sparsedist** \ help - **--sparsedistparams** \ help - **--split** \ help - **--\[no\]ssort** help - **--sspenalty** \ help - **--\[no\]stable\_sort** help - **--staralign** \ help - **--stepwords** \ help - **--strand** \ help - **--targetfract** \ help - **--targetlen** \ help - **--tmpdir** \ help - **--\[no\]trace** help - **--tracestate** \ help - **--\[no\]trunclabels** help - **--\[no\]twohit** help - **--uc** \ help - **--uc2clstr** \ help - **--uc2fasta** \ help - **--uc2fastax** \ help - **--uchime** \ help - **--uchimealns** \ help - **--uchimeout** \ help - **--\[no\]ucl** help - **--uhire** \ help - **--ungapped** help - **--userfields** \ help - **--userout** \ help - **--usersort** help - **--uslink** \ help - **--\[no\]usort** help - **--utax** \ help - **--\[no\]verbose** help - **--version** Show version and exit. - **--w** \ help - **--weak\_evalue** \ help - **--weak\_id** \ help - **--\[no\]wordcountreject** help - **--\[no\]wordweight** help - **--xa** \ help - **--xdrop\_g** \ help - **--xdrop\_nw** \ help - **--xdrop\_u** \ help - **--xdrop\_ug** \ help - **--xframe** \ help - **--xlat** help - **--xn** \ help ## AUTHOR Robert C. Edgar ## SEE ALSO http://www.drive5.com/uchime