wgsim(1)

💜 wgsim(1) — whole-genome sequencing read simulator 💜

okay bestie, so this is a wgsim manual page — it comes from the Bioinformatics tools corner of the world, and it simulates whole-genome sequencing reads for you. It's giving "pretend sequencer, but make it cute" ✨

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🎀 NAME 🎀

wgsim — whole-genome sequencing read simulator. that's the whole vibe. no cap. 💅

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🦋 SYNOPSIS 🦋

wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>

• <in.ref.fa> — bestie, this has to be a fasta file containing a reference genome. like, required. it's the blueprint, the main character, the reference genome moment. 🧬
• <out.read1.fq> and <out.read2.fq> — these two are your first and second read output files. the pair. the duo. the ship that sails together. 🫶

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✨ OPTIONS ✨

every single flag, coming right up, and yes i listed them all because i'm nothing if not thorough 💖

• -e FLOAT — base error rate, and it's [0.000] by default. so out of the box: zero errors, perfect little reads, flawless queen energy. 👑
• -d INT — outer distance between the two ends, default [500]. that's how far apart the two ends of a pair sit — the outer distance, not the insert. iykyk.
• -s INT — standard deviation, default [50]. the wiggle factor. the spread. the "it's approximately this but life is chaotic" number. 🌸
• -N INT — number of read pairs, default [1000000]. that's one million pairs, bestie. a million. go big or go home. 🔥
• -1 INT — length of the first read, default [70].
• -2 INT — length of the second read, default [70]. two separate flags for two separate reads because they're individuals, they're not the same, respect them. 💅
• -r FLOAT — rate of mutations, default [0.0010]. spice level of the genome. lowkey spicy.
• -R FLOAT — fraction of indels, default [0.15]. what share of the mutations are indels rather than the other kind.
• -X FLOAT — probability an indel is extended, default [0.30]. the extension probability — the "does this indel keep going" odds.
• -S INT — seed for the random generator, default [-1]. the reproducibility lever, fr fr. set it and your randomness becomes reliable randomness. iconic.
• -A FLOAT — discard a read if the fraction of ambiguous bases is higher than FLOAT, default [0.05]. so: too many N's, and it's out. bye. 🙈
• -h — haplotype mode. that's it, that's the whole description, it activates haplotype mode.

💀 reminder from the page itself: Parameter defaults are given in square brackets. so those [...] numbers up there? those are the defaults. i put them in literally every bullet so you'd never have to guess. 🫶

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🌈 AUTHOR 🌈

• Copyright 2008 Genome Research Limited.
• Copyright 2011 Heng Li.
• wgsim is part of samtools, over at https://github.com/samtools/samtools — go say hi, the repo is right there. ⭐

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okay that's the whole page, and now the cute little sign-off: this one's from samtools-1.24, dated 9 July 2026 — so go forth, simulate those reads, and remember: the defaults are in the brackets, the fasta is mandatory, and you're doing amazing sweetie 🍓🧚💜