NAME

       stellar - the SwifT Exact LocaL AligneR

       SYNOPSIS

              stellar [OPTIONS] <FASTA FILE 1> <FASTA FILE 2>

       DESCRIPTION

              STELLAR implements the SWIFT filter algorithm (Rasmussen et al., 2006) and a verification step for
              the  SWIFT  hits  that  applies  local  alignment,  gapped X-drop extension, and extraction of the
              longest epsilon-match.

              Input to STELLAR are two files, each containing one  or  more  sequences  in  FASTA  format.  Each
              sequence  from  file  1 will be compared to each sequence in file 2. The sequences from file 1 are
              used as database, the sequences from file 2 as queries.

              (c) 2010-2012 by Birte Kehr

       -h, --help

              Displays this help message.

       --version

              Display version information

              Main Options:

       -e, --epsilon NUM

              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength NUM

              Minimal length of epsilon-matches. In range [0..inf]. Default: 100.

       -f, --forward

              Search only in forward strand of database.

       -r, --reverse

              Search only in reverse complement of database.

       -a, --alphabet STR

              Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One  of  dna,  dna5,  rna,
              rna5, protein, and char.

       -v, --verbose

              Set verbosity mode.

              Filtering Options:

       -k, --kmer NUM

              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriod NUM

              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLength NUM

              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCut NUM

              k-mer overabundance cut ratio. In range [0..1]. Default: 1.

              Verification Options:

       -x, --xDrop NUM

              Maximal x-drop for extension. Default: 5.

       -vs, --verification STR

              Verification   strategy:  exact  or  bestLocal  or  bandedGlobal  One  of  exact,  bestLocal,  and
              bandedGlobal. Default: exact.

       -dt, --disableThresh NUM

              Maximal number of verified matches before disabling verification for one query  sequence  (default
              infinity). In range [0..inf].

       -n, --numMatches NUM

              Maximal  number  of  kept  matches per query and database. If STELLAR finds more matches, only the
              longest ones are kept. Default: 50.

       -s, --sortThresh NUM

              Number of matches triggering removal of duplicates. Choose  a  smaller  value  for  saving  space.
              Default: 500.

              Output Options:

       -o, --out FILE

              Name of output file. Valid filetypes are: gff and txt. Default: stellar.gff.

       -od, --outDisabled FILE

              Name  of  output  file  for  disabled query sequences. Valid filetypes are: fa and FASTA. Default:
              stellar.disabled.fasta.

       REFERENCES

              Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local  alignments.  BMC  Bioinformatics,
              12(Suppl 9):S15, 2011.

       VERSION

              stellar version: 1.3 Last update October 2012

stellar 1.4.1+dfsg                                October 2014                                        STELLAR(1)