.TH STELLAR 1 "" "stellar 1.4.11 [tarball]" ""
.SH NAME
stellar \- the SwifT Exact LocaL AligneR
.SH SYNOPSIS
\fBstellar\fP [\fIOPTIONS\fP] <\fIFASTA FILE 1\fP> <\fIFASTA FILE 2\fP>
.SH 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.
.sp
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.
.sp
(c) 2010-2012 by Birte Kehr
.SH REQUIRED ARGUMENTS
.TP
\fBFASTA_FILE_1\fP \fIINPUT_FILE\fP
 Valid filetypes are: \fI.fasta\fP and \fI.fa\fP.
.TP
\fBFASTA_FILE_2\fP \fIINPUT_FILE\fP
 Valid filetypes are: \fI.fasta\fP and \fI.fa\fP.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options:
.TP
\fB-e\fP, \fB--epsilon\fP \fIDOUBLE\fP
Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: \fI0.05\fP.
.TP
\fB-l\fP, \fB--minLength\fP \fIINTEGER\fP
Minimal length of epsilon-matches. In range [0..inf]. Default: \fI100\fP.
.TP
\fB-f\fP, \fB--forward\fP
Search only in forward strand of database.
.TP
\fB-r\fP, \fB--reverse\fP
Search only in reverse complement of database.
.TP
\fB-a\fP, \fB--alphabet\fP \fISTRING\fP
Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of \fIdna\fP, \fIdna5\fP, \fIrna\fP, \fIrna5\fP, \fIprotein\fP, and \fIchar\fP.
.TP
\fB-v\fP, \fB--verbose\fP
Set verbosity mode.
.SS Filtering Options:
.TP
\fB-k\fP, \fB--kmer\fP \fIINTEGER\fP
Length of the q-grams (max 32). In range [1..32].
.TP
\fB-rp\fP, \fB--repeatPeriod\fP \fIINTEGER\fP
Maximal period of low complexity repeats to be filtered. Default: \fI1\fP.
.TP
\fB-rl\fP, \fB--repeatLength\fP \fIINTEGER\fP
Minimal length of low complexity repeats to be filtered. Default: \fI1000\fP.
.TP
\fB-c\fP, \fB--abundanceCut\fP \fIDOUBLE\fP
k-mer overabundance cut ratio. In range [0..1]. Default: \fI1\fP.
.SS Verification Options:
.TP
\fB-x\fP, \fB--xDrop\fP \fIDOUBLE\fP
Maximal x-drop for extension. Default: \fI5\fP.
.TP
\fB-vs\fP, \fB--verification\fP \fISTRING\fP
Verification strategy: exact or bestLocal or bandedGlobal One of \fIexact\fP, \fIbestLocal\fP, and \fIbandedGlobal\fP. Default: \fIexact\fP.
.TP
\fB-dt\fP, \fB--disableThresh\fP \fIINTEGER\fP
Maximal number of verified matches before disabling verification for one query sequence (default infinity). In range [0..inf].
.TP
\fB-n\fP, \fB--numMatches\fP \fIINTEGER\fP
Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept. Default: \fI50\fP.
.TP
\fB-s\fP, \fB--sortThresh\fP \fIINTEGER\fP
Number of matches triggering removal of duplicates. Choose a smaller value for saving space. Default: \fI500\fP.
.SS Output Options:
.TP
\fB-o\fP, \fB--out\fP \fIOUTPUT_FILE\fP
Name of output file. Valid filetypes are: \fI.txt\fP and \fI.gff\fP. Default: \fIstellar.gff\fP.
.TP
\fB-od\fP, \fB--outDisabled\fP \fIOUTPUT_FILE\fP
Name of output file for disabled query sequences. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression. Default: \fIstellar.disabled.fasta\fP.
.SH REFERENCES
Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.