RAZERS(1)

💖 razers(1) — Fast Read Mapping with Sensitivity Control 💖

okay bestie, sit DOWN, because razers is about to become your new hyperfixation 🧚✨ (it lives in section 1 of the manual, hence the (1), iykyk)

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🌸 NAME 🌸

razers — Fast Read Mapping with Sensitivity Control

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🦋 SYNOPSIS 🦋

razers [OPTIONS] <GENOME FILE> <READS FILE>
razers [OPTIONS] <GENOME FILE> <MP-READS FILE1> <MP-READS FILE2>

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✨ DESCRIPTION ✨

RazerS is a versatile full-sensitive read mapper based on a k-mer counting filter. It supports single and paired-end mapping, and it optimally parametrizes the filter based on a user-defined minimal sensitivity. Wanna know more? Go look at https://www.seqan.de/apps/razers3P 💅

Input to RazerS 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. And listen — use - to read single-end reads from stdin. slay.

(c) Copyright 2009 by David Weese. 🫶

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👑 REQUIRED ARGUMENTS 👑

• ARGUMENT 0 INPUT_FILE — A reference genome file. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .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[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. 🌈

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🌟 OPTIONS 🌟

bestie there are like. SO many options. every single one is here, no skips, periodt 💀

• -h, --help — Display the help message. 🆘
• --version — Display version information.

🎀 Main Options 🎀

• -f, --forward — Map reads only to forward strands. ➡️
• -r, --reverse — Map reads only to reverse strands. ⬅️
• -i, --percent-identity DOUBLE — Percent identity threshold. In range [50..100]. Default: 92.
• -rr, --recognition-rate DOUBLE — 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 — that's literally -m 1 -dr 0 -pa, all bundled up. 💅
• -tr, --trim-reads INTEGER — Trim reads to given length. Default: off. In range [14..inf].
• -o, --output OUTPUT_FILE — Change output filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. Valid filetypes are: .razers, .gff, .fasta, .fa, and .eland. 📝
• -v, --verbose — Verbose mode.
• -vv, --vverbose — Very verbose mode. (yes, VERY. it's giving main character energy 🫶)

💜 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..2]. Default: 0.
• -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.

🍓 Filtration Options 🍓

• -s, --shape STRING — Manually set k-mer shape. Default: 11111111111.
• -t, --threshold INTEGER — Manually set minimum k-mer count threshold. In range [1..inf].
• -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. (trade-offs, bestie, we love a lil sacrifice 🙈)

⭐ Verification Options ⭐

• -mN, --match-N — N matches all other characters. Default: N matches nothing.
• -ed, --error-distr STRING — Write error distribution to FILE.
• -mcl, --min-clipped-len INTEGER — Set minimal read length for read clipping. In range [0..inf]. Default: 0.
• -qih, --quality-in-header — Quality string in fasta header.

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🌈 FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES 🌈

RazerS supports various output formats. The output format is detected automatically from the file name suffix. no cap. 🔍

• .razers — Razer format
• .fa, .fasta — Enhanced Fasta format
• .eland — Eland format
• .gff — GFF 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!). 👀

The way matches are sorted in the output file can be changed with the -so option for the following formats: razer, fasta, sam, and amos. 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.

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🔥 EXAMPLES 🔥

• razers example/genome.fa example/reads.fa -id -a -mN -v Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything. ✨
• razers example/genome.fa example/reads.fa example/reads2.fa -id -mN Map paired-end reads with up to 4% errors, indels, and output concordantly mapped pairs within default library size. Ns are considered to match everything. ✨

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and that's the whole thing, bestie, you ATE that documentation 🍽️💅 this gorgeousness is razers version 1.5.12 [tarball] — go forth and map, you absolute icon 👑💖🦋