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stellar - the SwifT Exact LocaL AligneR




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


Valid filetypes are: .fasta and .fa.
Valid filetypes are: .fasta and .fa.


-h, --help
Display the help message.
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.


Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.
stellar 1.4.10 [tarball]