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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 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
AUTHOR
Robert C. Edgar
SEE ALSO
http://www.drive5.com/uchime