stellar1
The swift exact local aligner
Usage
stellar [OPTIONS]
<FASTA
FILE
1>
<FASTA
FILE
2>
Overview
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_1INPUT_FILE-
Valid filetypes are: .fasta and .fa.
FASTA_FILE_2INPUT_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.
History
- Debian 13 (Trixie) to Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)
- Debian 8 (Jessie)
--abundanceCut since Debian 10 (Buster);
--alphabet since Debian 10 (Buster);
--disableThresh since Debian 10 (Buster);
--epsilon since Debian 10 (Buster);
--forward since Debian 10 (Buster);
--help since Debian 10 (Buster);
--kmer since Debian 10 (Buster);
--minLength since Debian 10 (Buster);
--numMatches since Debian 10 (Buster);
--out since Debian 10 (Buster);
--outDisabled since Debian 10 (Buster);
--repeatLength since Debian 10 (Buster);
--repeatPeriod since Debian 10 (Buster);
--reverse since Debian 10 (Buster);
--sortThresh since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--verification since Debian 10 (Buster);
--version since Debian 10 (Buster);
--xDrop since Debian 10 (Buster);
-a since Debian 10 (Buster);
-c since Debian 10 (Buster);
-dt since Debian 10 (Buster);
-e since Debian 10 (Buster);
-f since Debian 10 (Buster);
-h since Debian 10 (Buster);
-k since Debian 10 (Buster);
-l since Debian 10 (Buster);
-n since Debian 10 (Buster);
-o since Debian 10 (Buster);
-od since Debian 10 (Buster);
-r since Debian 10 (Buster);
-rl since Debian 10 (Buster);
-rp since Debian 10 (Buster);
-s since Debian 10 (Buster);
-v since Debian 10 (Buster);
-vs since Debian 10 (Buster);
-x since Debian 10 (Buster).