NAME¶

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-check BOOL

Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.

--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: .fasta and .fa. 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

Last update: stellar version: 1.4.9 [tarball] SeqAn version: 2.3.1