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razers3 - Faster, fully sensitive read mapping




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 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.


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.
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.


-h, --help
Display the help message.
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.
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.
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.


RazerS 3 supports various output formats. The output format is detected automatically from the file name suffix.
Razer format
.fa, .fasta
Enhanced Fasta format
Eland format
GFF format
SAM format
BAM format
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:

Use Fasta id.
Enumerate beginning with 1.
Use the read sequence (only for short reads!).
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:

1. read number, 2. genome position
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:

Gap space. Gaps between characters are counted from 0.
Position space. Characters are counted from 1.


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]