STELLAR(1)

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.