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STELLAR(1) User Commands 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
-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
September 2014 stellar 1.4.1+dfsg