Man page - stellar(1)
Packages contains this manual
- rabema_evaluate(1)
- alf(1)
- mason_materializer(1)
- pair_align(1)
- gustaf(1)
- stellar(1)
- razers3(1)
- sak(1)
- yara_indexer(1)
- mason_frag_sequencing(1)
- micro_razers(1)
- rabema_prepare_sam(1)
- insegt(1)
- rabema_build_gold_standard(1)
- splazers(1)
- seqan_tcoffee(1)
- yara_mapper(1)
- tree_recon(1)
- mason_genome(1)
- mason_methylation(1)
- razers(1)
- snp_store(1)
apt-get install seqan-apps
Manual
STELLAR
NAMESYNOPSIS
DESCRIPTION
REQUIRED ARGUMENTS
OPTIONS
Main Options:
Filtering Options:
Verification Options:
Output Options:
REFERENCES
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.