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SPLAZERS(1) | User Commands | SPLAZERS(1) |
NAMEΒΆ
splazers - Split-map read sequencesSYNOPSIS
- 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.
- 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.
OPTIONS
-h, --help
- Display the help message.
--version-check BOOL
- 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.
--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.
VERSION
- Last update: splazers version: 1.3.6 [tarball] SeqAn version: 2.3.1
June 2017 | splazers 2.3.1+dfsg-4 |