table of contents
| STELLAR(1) | 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.
| stellar 1.4.11 [tarball] |