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