RAZERS3(1)

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version 2.5.2 · 2 versions
, in ubuntu stonking

💖 RAZERS3(1) — the razers3 page, bestie edition 💖

okay so. section 1, general commands. this is razers3, and no cap, it's about to be your new favorite read mapper. let's go 🦋

✨ NAME ✨

razers3 — Faster, fully sensitive read mapping 🧬💅

🌸 SYNOPSIS 🌸

razers3 [OPTIONS] <GENOME FILE> <READS FILE>
razers3 [OPTIONS] <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>

👑 DESCRIPTION 👑

RazerS 3 ate and left no crumbs: it's a versatile, full-sensitive read mapper built on k-mer counting and seeding filters. It does single-end and paired-end mapping, it does shared-memory parallelism, and the way it optimally parametrizes the filter based on a minimal sensitivity you pick yourself? iconic. genuinely iconic. go look at https://www.seqan.de/apps/razers3 for more, iykyk 💜

What you feed it: a reference genome file, plus either one file of single-end reads or two files holding the left and right mates of paired-end reads. And here's a cute trick — pass - and it reads single-end reads straight from stdin 🍓

(c) Copyright 2009-2026 by David Weese.

🎀 REQUIRED ARGUMENTS 🎀

  • ARGUMENT 0 INPUT_FILE — this is your reference genome file, periodt. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of these extensions: gz, bz2, and bgzf — those give you transparent (de)compression, slay 🔥
  • READS List of INPUT_FILE's — either one file (single-end) or two files (paired-end) of reads. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of these extensions: gz, bz2, and bgzf for transparent (de)compression 💖

✨ OPTIONS ✨

  • -h, --help — display the help message. bestie behavior, always read the help 🫶
  • --version — display version information. who even are you (affectionate)

💅 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. that's literally -m 1 -dr 0 -pa btw, cute lil shorthand ✨
  • -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. it's giving main character energy 👑

🌈 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, bestie 👇). 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). no shortening, no gatekeeping 💅
  • -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. don't skip it.

🧚 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, and the way it knows which one you want is vibe check on the file name suffix — automatic, no cap.

  • .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 🔥

okay these are the moments, bestie. copy them, run them, live them 💖

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. 👑

🫶 reminder that this whole page is razers3 3.5.12 [tarball] — that's the version and where it came from, and it's dated to match the original page. go map something iconic, bestie. mwah 💅✨💖
📦 where this page comes from