菜单
Polish genome assemblies and fix small errors using short-read BAM evidence. Use after mapping Illumina reads to a draft assembly (including long-read drafts). Upstream: https://github.com/broadinstitute/pilon.
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 pilon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 | pilon |
| description | Polish genome assemblies and fix small errors using short-read BAM evidence. Use after mapping Illumina reads to a draft assembly (including long-read drafts). Upstream: https://github.com/broadinstitute/pilon. |
| license | MIT |
| category | analysis-tools |
| tags | ["polish","assembly","short-read"] |
| upstream | https://github.com/broadinstitute/pilon |
| stage | assembly |
Upstream: broadinstitute/pilon
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014). https://doi.org/10.1371/journal.pone.0112963
Pilon uses short-read alignments to correct SNPs/indels and optionally fill gaps. Requires high-quality BAM (Bowtie2/BWA) to the draft. Over-polishing heterogeneous metagenome contigs can erase true strain variation — prefer on isolate-like MAGs or low-complexity drafts, not blindly on all community contigs.
conda install -c bioconda pilon bowtie2 samtools
bowtie2-build draft.fa temp/polish/draft
bowtie2 -x temp/polish/draft -1 R1.fq.gz -2 R2.fq.gz -p 16 \
| samtools sort -@ 8 -o temp/polish/illumina.bam
samtools index temp/polish/illumina.bam
pilon --genome draft.fa --frags temp/polish/illumina.bam \
--output draft.pilon --outdir temp/polish --threads 16
bowtie2 · samtools · racon · quast · megahit · metaflye