YARA_INDEXER(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

✨ YARA_INDEXER(1) ✨

okay so bestie, welcome to the yara_indexer manual page 💖 this is the YARA_INDEXER(1) vibe, and we're gonna get you right.

🌸 NAME 🌸

yara_indexer — Yara Indexer. that's it, that's the name, short and iconic 💅

🦋 SYNOPSIS 🦋

yara_indexer [OPTIONS] <REFERENCE FILE>

like… that's the whole shape of it. you give it options, you give it a reference file. slay.

🎀 DESCRIPTION 🎀

Yara — Yet Another Read Aligner. yes bestie, that's the actual name, they went for the recursive acronym and honestly? respect 🫶

if you want the whole lore, it's over at https://www.seqan.de/apps/yara — go read, it's giving documentation.

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

no cap, those are the credits, we keep them because legends deserve their flowers 👑

💖 REQUIRED ARGUMENTS 💖

  • REFERENCE_FILE, INPUT_FILE — a reference genome file. and bestie, she is picky about filetypes, so listen up. valid ones 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. so like, .fasta.gz? valid. .fa.bz2? also valid. she handles the compression for you, no manual unzipping, no stress 🧚

⭐ OPTIONS ⭐

  • -h, --help — displays the help message. your lil "wait what does this do" button, we love her 🙈
  • --version — displays version information.
  • -v, --verbose — displays verbose output. for when you want the program to actually tell you what it's doing instead of just staring at you 💀

🍓 Output Options 🍓

  • -o, --output-prefix OUTPUT_PREFIX — specify a filename prefix for the reference genome index. Default: use the filename prefix of the reference genome. so if you don't say anything, she just reuses the reference's own prefix, easy ✨
  • -td, --tmp-dir STRING — specify a temporary directory where to construct the index. Default: use the output directory. so if you don't hand her a temp spot, she'll just do her lil construction work in the output directory, no drama 🎀

and that's the whole page bestie, you're now certified in yara_indexer 💅💜

this was yara_indexer 1.0.6 [tarball], the YARA_INDEXER(1) manual — go index something iconic 👑🌸

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