.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH STELLAR "1" "June 2017" "stellar 2.3.1+dfsg-4" "User Commands"
.SH NAME
stellar \- the SwifT Exact LocaL AligneR
.PP
SYNOPSIS
.IP
stellar [OPTIONS] <FASTA FILE 1> <FASTA FILE 2>
.PP
DESCRIPTION
.IP
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.
.IP
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.
.IP
(c) 2010\-2012 by Birte Kehr
.PP
REQUIRED ARGUMENTS
.IP
FASTA_FILE_1 INPUT_FILE
.IP
Valid filetypes are: .fasta and .fa.
.IP
FASTA_FILE_2 INPUT_FILE
.IP
Valid filetypes are: .fasta and .fa.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options:
.HP
\fB\-e\fR, \fB\-\-epsilon\fR DOUBLE
.IP
Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default:
0.05.
.HP
\fB\-l\fR, \fB\-\-minLength\fR INTEGER
.IP
Minimal length of epsilon\-matches. In range [0..inf]. Default: 100.
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
Search only in forward strand of database.
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
Search only in reverse complement of database.
.HP
\fB\-a\fR, \fB\-\-alphabet\fR STRING
.IP
Alphabet type of input sequences (dna, rna, dna5, rna5, protein,
char). One of dna, dna5, rna, rna5, protein, and char.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Set verbosity mode.
.IP
Filtering Options:
.HP
\fB\-k\fR, \fB\-\-kmer\fR INTEGER
.IP
Length of the q\-grams (max 32). In range [1..32].
.HP
\fB\-rp\fR, \fB\-\-repeatPeriod\fR INTEGER
.IP
Maximal period of low complexity repeats to be filtered. Default: 1.
.HP
\fB\-rl\fR, \fB\-\-repeatLength\fR INTEGER
.IP
Minimal length of low complexity repeats to be filtered. Default:
1000.
.HP
\fB\-c\fR, \fB\-\-abundanceCut\fR DOUBLE
.IP
k\-mer overabundance cut ratio. In range [0..1]. Default: 1.
.IP
Verification Options:
.HP
\fB\-x\fR, \fB\-\-xDrop\fR DOUBLE
.IP
Maximal x\-drop for extension. Default: 5.
.HP
\fB\-vs\fR, \fB\-\-verification\fR STRING
.IP
Verification strategy: exact or bestLocal or bandedGlobal One of
exact, bestLocal, and bandedGlobal. Default: exact.
.HP
\fB\-dt\fR, \fB\-\-disableThresh\fR INTEGER
.IP
Maximal number of verified matches before disabling verification for
one query sequence (default infinity). In range [0..inf].
.HP
\fB\-n\fR, \fB\-\-numMatches\fR INTEGER
.IP
Maximal number of kept matches per query and database. If STELLAR
finds more matches, only the longest ones are kept. Default: 50.
.HP
\fB\-s\fR, \fB\-\-sortThresh\fR INTEGER
.IP
Number of matches triggering removal of duplicates. Choose a smaller
value for saving space. Default: 500.
.IP
Output Options:
.HP
\fB\-o\fR, \fB\-\-out\fR OUTPUT_FILE
.IP
Name of output file. Valid filetypes are: .txt and .gff. Default:
stellar.gff.
.HP
\fB\-od\fR, \fB\-\-outDisabled\fR OUTPUT_FILE
.IP
Name of output file for disabled query sequences. Valid filetypes
are: .fasta and .fa. Default: stellar.disabled.fasta.
.PP
REFERENCES
.IP
Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local
alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.
.PP
VERSION
.IP
Last update:
stellar version: 1.4.9 [tarball]
SeqAn version: 2.3.1