菜单
Architecture-aware faster BWA-MEM for Illumina reads to contigs/genomes. Use when a BWA-MEM workflow is required but throughput must improve, or when migrating from classic bwa mem. Upstream: https://github.com/bwa-mem2/bwa-mem2. Index format is NOT compatible with classic bwa index.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill bwa-mem2命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks. Upstream: https://github.com/tseemann/abricate. Route via cge-finders / microbial-mining; official CGE CLI still via resfinder/plasmidfinder when phenotype mapping or PointFinder is required.
Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for clinical/One-Health isolate typing and plasmid-borne AMR context — not community-wide dark-matter discovery. Child skills: plasmidfinder, resfinder, pointfinder, disinfinder, virulencefinder, mobileelementfinder, pmlst, staramr, abricate, mlst. Complements genomad, mob-suite, rgi, mobileog. Route via microbial-mining.
DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db. Route via cge-finders / resfinder / microbial-mining.
基于 SOC 职业分类
正在显示 SKILL.md
| name | bwa-mem2 |
| description | Architecture-aware faster BWA-MEM for Illumina reads to contigs/genomes. Use when a BWA-MEM workflow is required but throughput must improve, or when migrating from classic bwa mem. Upstream: https://github.com/bwa-mem2/bwa-mem2. Index format is NOT compatible with classic bwa index. |
| license | MIT |
| category | analysis-tools |
| tags | ["mapping","alignment","short-read","bwa"] |
| upstream | https://github.com/bwa-mem2/bwa-mem2 |
| stage | mapping |
Upstream: bwa-mem2/bwa-mem2
Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. IEEE IPDPS 314–324 (2019). https://doi.org/10.1109/IPDPS.2019.00041
Classic algorithm context: Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv (2013). https://doi.org/10.48550/arXiv.1303.3997
BWA-MEM2 keeps the MEM mapping model familiar to BWA users while speeding
alignment on modern CPUs. Critical pitfall: bwa-mem2 index ≠ bwa index —
never point bwa-mem2 mem at a classic BWA index (or the reverse).
For new metagenome coverage projects, strobealign or bowtie2 may be simpler;
choose BWA-MEM2 when SOPs/scripts already assume BWA-MEM flags and SAM fields.
| Requirement | Minimum | Recommended |
|---|---|---|
| Index | From bwa-mem2 index | Rebuild if upgrading major version |
| RAM | Index ~ reference size class | Large co-assemblies need big nodes |
conda install -c bioconda bwa-mem2 samtools
bwa-mem2 index contigs.fa
bwa-mem2 mem -t 16 contigs.fa \
temp/hr/${id}_1.fastq temp/hr/${id}_2.fastq \
2> temp/map/${id}.bwa-mem2.log \
| samtools sort -@ 8 -o temp/map/${id}.bam
samtools index temp/map/${id}.bam
| Option | Guidance |
|---|---|
-t | Threads |
-R | Read group (@RG) when merging multi-lane BAMs |
-K | Process chunk size; raise on huge inputs if supported |
Need BWA-MEM-like mapping?
├─ Legacy classic bwa only available → bwa
├─ Speed on modern CPUs → bwa-mem2
└─ Greenfield metagenome coverage → strobealign or bowtie2
| Symptom | Action |
|---|---|
| Index load errors | Rebuild with bwa-mem2 index |
| Divergent SM tags | Set -R consistently across lanes |
| Huge unsorted SAM | Stream to samtools sort (never dump SAM) |
bwa · bowtie2 · strobealign · samtools · coverm · metabat2