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

REQUIRED ARGUMENTS

       FASTA_FILE_1 INPUT_FILE
               Valid filetypes are: .fasta and .fa.

       FASTA_FILE_2 INPUT_FILE
               Valid filetypes are: .fasta and .fa.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options:
       -e, --epsilon DOUBLE
              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength INTEGER
              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 STRING
              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 INTEGER
              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriod INTEGER
              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLength INTEGER
              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCut DOUBLE
              k-mer overabundance cut ratio. In range [0..1]. Default: 1.

   Verification Options:
       -x, --xDrop DOUBLE
              Maximal x-drop for extension. Default: 5.

       -vs, --verification STRING
              Verification   strategy:  exact  or  bestLocal  or  bandedGlobal  One  of  exact,  bestLocal,  and
              bandedGlobal. Default: exact.

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

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

       -s, --sortThresh INTEGER
              Number of matches triggering removal of duplicates. Choose  a  smaller  value  for  saving  space.
              Default: 500.

   Output Options:
       -o, --out OUTPUT_FILE
              Name of output file. Valid filetypes are: .txt and .gff. Default: stellar.gff.

       -od, --outDisabled OUTPUT_FILE
              Name  of  output  file  for  disabled  query  sequences.  Valid filetypes are: .sam[.*], .raw[.*],
              .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam,  where
              *  is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. Default:
              stellar.disabled.fasta.

REFERENCES

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

stellar 1.4.11 [tarball]                                                                              STELLAR(1)