NAME
splazers - Split-map read sequences
SYNOPSIS
splazers [OPTIONS] <GENOME FILE> <READS FILE>
splazers [OPTIONS] <GENOME FILE> <READS FILE 1> <READS FILE 2>
DESCRIPTION
SplazerS uses a prefix-suffix mapping strategy to split-map read sequences.If a SAM file of mapped reads is given as input, all unmapped but anchoredreads are split-mapped onto anchoring target regions (specify option -an),if a Fasta/q file of reads is given, reads are split-mapped onto the wholereference sequence.
(c) Copyright 2010 by Anne-Katrin Emde.
REQUIRED ARGUMENTS
- ARGUMENT 0 INPUT_FILE
-
A reference genome file. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
- READS List of INPUT_FILE's
-
Either one (single-end) or two (paired-end) read files. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
OPTIONS
- -h, --help
-
Display the help message.
- --version
-
Display version information.
Main Options::
- -o, --output OUTPUT_FILE
-
Change output filename. Default: <READS FILE>.result.
- -f, --forward
-
only compute forward matches
- -r, --reverse
-
only compute reverse complement matches
- -i, --percent-identity DOUBLE
-
Percent identity threshold. In range [50..100]. Default: 92.
- -rr, --recognition-rate DOUBLE
-
set the percent recognition rate In range [80..100]. Default: 99.
- -pd, --param-dir STRING
-
Read user-computed parameter files in the directory <DIR>.
- -id, --indels
-
Allow indels. Default: mismatches only.
- -ll, --library-length INTEGER
-
Paired-end library length. In range [1..inf]. Default: 220.
- -le, --library-error INTEGER
-
Paired-end library length tolerance. In range [0..inf]. Default: 50.
- -m, --max-hits INTEGER
-
Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
- --unique
-
Output only unique best matches (-m 1 -dr 0 -pa).
- -tr, --trim-reads INTEGER
-
Trim reads to given length. Default: off. In range [14..inf].
- -mcl, --min-clipped-len INTEGER
-
min. read length for read clipping In range [1..inf]. Default: 0.
- -qih, --quality-in-header
-
quality string in fasta header
- -ou, --outputUnmapped OUTPUT_FILE
-
output filename for unmapped reads
- -v, --verbose
-
verbose mode
- -vv, --vverbose
-
very verbose mode
Output Format Options::
- -a, --alignment
-
dump the alignment for each match
- -pa, --purge-ambiguous
-
purge reads with more than max-hits best matches
- -dr, --distance-range INTEGER
-
only consider matches with at most NUM more errors compared to the best (default output all)
- -of, --output-format INTEGER
-
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In range [0..4].
- -gn, --genome-naming INTEGER
-
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
- -rn, --read-naming INTEGER
-
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
- -so, --sort-order INTEGER
-
Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.
- -pf, --position-format INTEGER
-
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0.
Split Mapping Options::
- -sm, --split-mapping INTEGER
-
min. match length for prefix/suffix mapping (to disable split mapping, set to 0) Default: 18.
- -maxG, --max-gap INTEGER
-
max. length of middle gap Default: 10000.
- -minG, --min-gap INTEGER
-
min. length of middle gap (for edit distance mapping about 10% of read length is recommended) Default: 0.
- -ep, --errors-prefix INTEGER
-
max. number of errors in prefix match Default: 1.
- -es, --errors-suffix INTEGER
-
max. number of errors in suffix match Default: 1.
- -gl, --genome-len INTEGER
-
genome length in Mb, for computation of expected number of random matches In range [-inf..10000]. Default: 3000.
- -an, --anchored
-
anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format
- -pc, --penalty-c INTEGER
-
percent of read length, used as penalty for split-gap Default: 2.
Filtration Options::
- -oc, --overabundance-cut INTEGER
-
Set k-mer overabundance cut ratio. In range [0..1].
- -rl, --repeat-length INTEGER
-
Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
- -tl, --taboo-length INTEGER
-
Set taboo length. In range [1..inf]. Default: 1.
- -lm, --low-memory
-
decrease memory usage at the expense of runtime
Verification Options:
- -mN, --match-N
-
N matches all other characters. Default: N matches nothing.
- -ed, --error-distr STRING
-
Write error distribution to FILE.