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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

              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 <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