bwa-mem2-dna-aligner SKILL.md skillA
bwa-mem2-dna-aligner from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/bwa-mem2-dna-aligner@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 13,984 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# BWA-MEM2 — DNA Short-Read Aligner ## Overview BWA-MEM2 aligns short DNA reads (Illumina, 50–250 bp) to a reference genome using the BWT-FM index. It is the standard aligner for whole-genome sequencing (WGS), whole-exome sequencing (WES), ChIP-seq, and ATAC-seq DNA alignment. BWA-MEM2 is 2× faster than the original BWA-MEM while producing identical results. It outputs SAM format with proper read group (`@RG`) headers required by GATK HaplotypeCaller and Picard tools. For paired-end reads, it marks proper pairs and resolves chimeric/split reads into supplementary alignments. ## When to Use - Aligning WGS or WES Illumina reads to a reference genome for variant calling (SNP, indel, SV) - ChIP-seq or ATAC-seq DNA alignment to produce BAM files for peak calling with MACS3 - Producing GATK-compatible BAM files with `@RG` read group tags - Aligning reads ≥ 50 bp; for shorter reads (< 50 bp), BWA-backtrack may be more appropriate - Re-aligning legacy FASTQ files to an updated reference genome assembly - Use **STAR** instead for RNA-seq reads that span splice junctions - Use **Bowtie2** as an alternative for local alignment or when index size must be minimized ## Prerequisites …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/bwa-mem2-dna-aligner@sha256:3d96b5b6f3ca8fcdThe line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_yxg3dkmmhtky5tyf)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 62 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 13,984 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 14,033 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 12,373 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13984 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yxg3dkmmhtky5tyf GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/bwa-mem2-dna-aligner GET https://markdownregistry.com/api/v1/blob/3d96b5b6f3ca8fcd429ce32bc4782b302a959d89c1344d498f15a3f2bc6c338f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.