YARA_MAPPER(1)

📦
version 2.5.2 · 3 versions
, in ubuntu stonking

💖 YARA_MAPPER — like, the manual, bestie 💖

okay so this is the man page for yara_mapper, from section 1 of the manual (yes, the classic "user commands" section, we love her). Sit down, grab a strawberry drink 🍓, and let's get you fluent in read alignment. No cap, it's easier than it looks.

✨ NAME ✨

yara_mapper — Yara Mapper. That's it, that's the name, she's iconic and she knows it 💅

🌸 SYNOPSIS 🌸

yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <SE-READS FILE>
yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <PE-READS FILE 1> <PE-READS FILE 2>

Two ways to run her: one single-end reads file, or two paired-end reads files. Choose your fighter 🦋

🎀 DESCRIPTION 🎀

Yara — Yet Another Read Aligner. The way she said "yet another" and then absolutely ate 😭

More lore lives at https://www.seqan.de/apps/yara — go read it, iykyk.

Legal besties, listen up:

  • (c) Copyright 2011-2026 by Enrico Siragusa.
  • (c) Copyright 2013 by NVIDIA Corporation.

👑 REQUIRED ARGUMENTS 👑

These aren't optional, bestie. She needs them. No skipping, fr fr.

  • REFERENCE_INDEX_PREFIX, INPUT_PREFIX — an indexed reference genome. That's your starting point, your main character foundation ✨
  • READS_FILE, List of INPUT_FILE's — either one single-end file, or two paired-end / mate-pair 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. See how generous she is with formats? Obsessed actually 🌈

💅 OPTIONS 💅

okay this is the big one. Forty-ish ways to tell her what you want. We're going through ALL of them, no summarising, that's a promise 🫶

  • -h, --help — Display the help message. When you're lost, she's there 💖
  • --version — Display version information. Receipts, basically.
  • -v, --verbose — Displays global statistics. The vibes, quantified ✨
  • -vv, --very-verbose — Displays extensive statistics for each batch of reads. Now she's telling you everything, and honestly? We listen. 👑

🎀 Output Options —

  • -o, --output-file OUTPUT_FILE — Specify an output file. Default: write the file to standard output. Valid filetypes are: .sam[.*] and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. Same energy as the input list, because consistency is hot 🔥
  • -f, --output-format STRING — Specify an output format. Note: when specifying the option --output-file, the output format is taken from the filename extension. One of bam, sam, sam.bgzf, sam.gz, and sam.bz2. Default: sam. She reads the extension, she doesn't argue, she's chill like that 💅
  • -rg, --read-group STRING — Specify a read group for all records in the SAM/BAM file. Default: none. Group chat for your reads, literally 🫶
  • -sm, --secondary-matches STRING — Specify whether to output secondary matches in the XA tag of the primary alignment, as separate secondary records, or to omit them. One of tag, record, and omit. Default: tag. Pick your delivery method, girlie ✨
  • -as, --align-secondary — Compute and output co- and suboptimal match alignments. Ignored if '-sa omit' is set. So if you set that, this one's just sitting there, not invited to the party 🙈
  • -ra, --rabema-alignments — Output alignments compatible with the Read Alignment BEnchMArk (RABEMA). Yes, the all-caps B is on purpose, that's the acronym being cute 💀

🔥 Mapping Options —

  • -e, --error-rate INTEGER — Consider alignments within this percentual number of errors. Increase this threshold to increase the number of mapped reads. Decrease this threshold to decrease the runtime. In range [0..10]. Default: 5. Trade-off queen 👑
  • -s, --strata-rate INTEGER — Consider suboptimal alignments within this percentual number of errors from the optimal alignment. Increase this threshold to increase the number of alternative alignments at the expense of runtime. In range [0..10]. More options, more time, classic 🌸
  • -sc, --strata-count INTEGER — Consider suboptimal alignments within this absolute number of errors from the optimal alignment. Increase this threshold to increase the number of alternative alignments at the expense of runtime. In range [0..127]. The absolute version of the previous one, and she goes up to 127, no cap.
  • -y, --sensitivity STRING — Sensitivity with respect to edit distance. Full sensitivity guarantees to find all considered alignments but increases runtime, low sensitivity decreases runtime by breaking such guarantee. One of low, high, and full. Default: high. Choose wisely bestie, because full will make you wait 😭

🦋 Paired-End Mapping Options —

  • -ll, --library-length INTEGER — Expected library length. Default: autodetected. In range [1..inf]. She'll figure it out herself if you let her ✨
  • -ld, --library-deviation INTEGER — Deviation from the expected library length. Default: autodetected. In range [1..inf]. Same deal, she's got instincts 💜
  • -i, --indel-rate INTEGER — Rescue unaligned ends within this percentual number of indels. In range [0..50]. Default: 25. Saving lost ends like a true friend 🫶
  • -ni, --no-indels — Turn off the rescue of unaligned ends containing indels. Sometimes you just don't want the rescue arc, and that's valid 🙈

🌈 Performance Options —

  • -t, --threads INTEGER — Specify the number of threads to use. In range [1..2048]. Default: 4. Crank it up if your machine is built different 🔥
quick vibe check: every range, default, filetype and option above is exactly as the original says. Don't guess, don't improvise, just read and slay ✨

and that's the whole page, bestie!! sign-off time 💖 — this manual is from yara_mapper 1.0.6 [tarball], and yeah, that's the whole flex. Go align something iconic. periodt. 💅✨🌈

📦 where this page comes from