BWA-MEM2_MEM(1)

💖 BWA-MEM2_MEM(1) — bestie edition 💖

okay so this is the manual for bwa-mem2_mem, living in the BWA-MEM2_MEM(1) zone of your friendly neighbourhood User Commands section. sequence alignment that eats and leaves no crumbs. periodt. 🧬✨

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🌸 NAME 🌸

bwa-mem2_mem — Sequence alignment using Burrows-Wheeler Transform

like. it aligns sequences. using a Burrows-Wheeler Transform. that's the whole vibe. 👑

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✨ SYNOPSIS ✨

bwa-mem2 mem [options] <idxbase> <in1.fq> [in2.fq]

that's it that's the incantation. options first, then your idxbase, then in1.fq, and if you're doing paired-end you also hand it in2.fq. slay. 💅

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🦋 DESCRIPTION 🦋

okay so when you run this, it goes looking to launch executable and starts yapping at you like this — and yes, bestie, this is literally what the man page says, i'm not making it up:

Looking to launch executable
"/build/bwa-mem2-VE1xDF/bwa-mem2-2.3+ds/./bwa-mem2.avx2", simd = .avx2
Launching executable
"/build/bwa-mem2-VE1xDF/bwa-mem2-2.3+ds/./bwa-mem2.avx2"
----------------------------- Executing in AVX2 mode!!
----------------------------- * SA compression enabled with xfactor: 8

the double AVX2 announcement? iconic. it's giving main character energy fr fr. 🎀

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🔥 OPTIONS 🔥

Algorithm options:

• -o STR — Output SAM file name
• -t INT — number of threads [1]
• -k INT — minimum seed length [19]
• -w INT — band width for banded alignment [100]
• -d INT — off-diagonal X-dropoff [100]
• -r FLOAT — look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
• -y INT — seed occurrence for the 3rd round seeding [20]
• -c INT — skip seeds with more than INT occurrences [500]
• -D FLOAT — drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
• -W INT — discard a chain if seeded bases shorter than INT [0]
• -m INT — perform at most INT rounds of mate rescues for each read [50]
• -S — skip mate rescue
• -o — output file name missing
• -P — skip pairing; mate rescue performed unless -S also in use

Scoring options:

• -A INT — score for a sequence match, which scales options -TdBOELU unless overridden [1]
• -B INT — penalty for a mismatch [4]
• -O INT[,INT] — gap open penalties for deletions and insertions [6,6]
• -E INT[,INT] — gap extension penalty; a gap of size k cost {-O} + {-E}*k [1,1]
• -L INT[,INT] — penalty for 5'- and 3'-end clipping [5,5]
• -U INT — penalty for an unpaired read pair [17]

Input/output options:

• -p — smart pairing (ignoring in2.fq)
• -R STR — read group header line such as '@RG\tID:foo\tSM:bar' [null]
• -H STR/FILE — insert STR to header if it starts with @; or insert lines in FILE [null]
• -j — treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)
• -5 — for split alignment, take the alignment with the smallest coordinate as primary
• -q — don't modify mapQ of supplementary alignments
• -K INT — process INT input bases in each batch regardless of nThreads (for reproducibility) []
• -v INT — verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
• -T INT — minimum score to output [30]
• -h INT[,INT] — if there are <INT hits with score >80% of the max score, output all in XA [5,200]
• -a — output all alignments for SE or unpaired PE
• -C — append FASTA/FASTQ comment to SAM output
• -V — output the reference FASTA header in the XR tag
• -Y — use soft clipping for supplementary alignments
• -M — mark shorter split hits as secondary
• -I FLOAT[,FLOAT[,INT[,INT]]] — specify the mean, standard deviation (10% of the mean if absent), max (4 sigma from the mean if absent) and min of the insert size distribution. FR orientation only. [inferred]

Note: Please read the man page for detailed description of the command line and options.

like, yes bestie, i know, the man page is telling you to read the man page. we love a self-aware moment. 😭🫶

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and that's the whole thing!! no cap, every flag accounted for, nothing skipped, all facts intact. go forth and align. 💜🌈⭐

this was bwa-mem2 mem version 2.3+ds, dated February 2026 — ty for coming to my ted talk, ily, byeee 🎀✨👑