| RAZERS3(1) | RAZERS3(1) |
NAME¶
razers3 - Faster, fully sensitive read mappingSYNOPSIS¶
razers3 [OPTIONS] <GENOME FILE> <READS FILE>razers3 [OPTIONS] <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>
DESCRIPTION¶
RazerS 3 is a versatile full-sensitive read mapper based on k-mer counting and seeding filters. It supports single and paired-end mapping, shared-memory parallelism, and optimally parametrizes the filter based on a user-defined minimal sensitivity. See http://www.seqan.de/projects/razers for more information.Input to RazerS 3 is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. Use - to read single-end reads from stdin.
(c) Copyright 2009-2014 by David Weese.
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:¶
- -i, --percent-identity DOUBLE
- Percent identity threshold. In range [50..100]. Default: 95.
- -rr, --recognition-rate DOUBLE
- Percent recognition rate. In range [80..100]. Default: 100.
- -ng, --no-gaps
- Allow only mismatches, no indels. Default: allow both.
- -f, --forward
- Map reads only to forward strands.
- -r, --reverse
- Map reads only to reverse strands.
- -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].
- -o, --output OUTPUT_FILE
- Mapping result filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. Valid filetypes are: .sam, .razers, .gff, .fasta, .fa, .eland, .bam, and .afg.
- -v, --verbose
- Verbose mode.
- -vv, --vverbose
- Very verbose mode.
Paired-end Options:¶
- -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.
Output Format Options:¶
- -a, --alignment
- Dump the alignment for each match (only razer or fasta format).
- -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.
- -gn, --genome-naming INTEGER
- Select how genomes are named (see Naming section below). In range [0..1]. Default: 0.
- -rn, --read-naming INTEGER
- Select how reads are named (see Naming section below). In range [0..3]. Default: 0.
- --full-readid
- Use the whole read id (don't clip after whitespace).
- -so, --sort-order INTEGER
- Select how matches are sorted (see Sorting section below). In range [0..1]. Default: 0.
- -pf, --position-format INTEGER
- Select begin/end position numbering (see Coordinate section below). In range [0..1]. Default: 0.
- -ds, --dont-shrink-alignments
- Disable alignment shrinking in SAM. This is required for generating a gold mapping for Rabema.
Filtration Options:¶
- -fl, --filter STRING
- Select k-mer filter. One of pigeonhole and swift. Default: pigeonhole.
- -mr, --mutation-rate DOUBLE
- Set the percent mutation rate (pigeonhole). In range [0..20]. Default: 5.
- -ol, --overlap-length INTEGER
- Manually set the overlap length of adjacent k-mers (pigeonhole). In range [0..inf].
- -pd, --param-dir STRING
- Read user-computed parameter files in the directory <DIR> (swift).
- -t, --threshold INTEGER
- Manually set minimum k-mer count threshold (swift). In range [1..inf].
- -tl, --taboo-length INTEGER
- Set taboo length (swift). In range [1..inf]. Default: 1.
- -s, --shape STRING
- Manually set k-mer shape.
- -oc, --overabundance-cut INTEGER
- Set k-mer overabundance cut ratio. In range [0..1]. Default: 1.
- -rl, --repeat-length INTEGER
- Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
- -lf, --load-factor DOUBLE
- Set the load factor for the open addressing k-mer index. In range [1..inf]. Default: 1.6.
Verification Options:¶
- -mN, --match-N
- N matches all other characters. Default: N matches nothing.
- -ed, --error-distr STRING
- Write error distribution to FILE.
- -mf, --mismatch-file STRING
- Write mismatch patterns to FILE.
Misc Options:¶
- -cm, --compact-mult DOUBLE
- Multiply compaction threshold by this value after reaching and compacting. In range [0..inf]. Default: 2.2.
- -ncf, --no-compact-frac DOUBLE
- Don't compact if in this last fraction of genome. In range [0..1]. Default: 0.05.
Parallelism Options:¶
- -tc, --thread-count INTEGER
- Set the number of threads to use (0 to force sequential mode). In range [0..inf]. Default: 1.
- -pws, --parallel-window-size INTEGER
- Collect candidates in windows of this length. In range [1..inf]. Default: 500000.
- -pvs, --parallel-verification-size INTEGER
- Verify candidates in packages of this size. In range [1..inf]. Default: 100.
- -pvmpc, --parallel-verification-max-package-count INTEGER
- Largest number of packages to create for verification per thread-1. In range [1..inf]. Default: 100.
- -amms, --available-matches-memory-size INTEGER
- Bytes of main memory available for storing matches. In range [-1..inf]. Default: 0.
- -mhst, --match-histo-start-threshold INTEGER
- When to start histogram. In range [1..inf]. Default: 5.
FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES¶
RazerS 3 supports various output formats. The output format is detected automatically from the file name suffix.- .razers
- Razer format
- .fa, .fasta
- Enhanced Fasta format
- .eland
- Eland format
- .gff
- GFF format
- .sam
- SAM format
- .bam
- BAM format
- .afg
- Amos AFG format
By default, reads and contigs are referred by their Fasta ids given in the input files. With the -gn and -rn options this behaviour can be changed:
- 0
- Use Fasta id.
- 1
- Enumerate beginning with 1.
- 2
- Use the read sequence (only for short reads!).
- 3
- Use the Fasta id, do NOT append /L or /R for mate pairs.
The way matches are sorted in the output file can be changed with the -so option for the following formats: razers, fasta, sam, and afg. Primary and secondary sort keys are:
- 0
- 1. read number, 2. genome position
- 1
- 1. genome position, 2. read number
The coordinate space used for begin and end positions can be changed with the -pf option for the razer and fasta formats:
- 0
- Gap space. Gaps between characters are counted from 0.
- 1
- Position space. Characters are counted from 1.
EXAMPLES¶
- razers3 -i 96 -tc 12 -o mapped.razers hg18.fa reads.fq
- Map single-end reads with 4% error rate using 12 threads.
- razers3 -i 95 -no-gaps -o mapped.razers hg18.fa reads.fq.gz
- Map single-end gzipped reads with 5% error rate and no indels.
- razers3 -i 94 -rr 95 -tc 12 -ll 280 --le 80 -o mapped.razers hg18.fa reads_1.fq reads_2.fq
- Map paired-end reads with up to 6% errors, 95% sensitivity, 12 threads, and only output aligned pairs with an outer distance of 200-360bp.
| razers3 3.5.8 [tarball] |