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Ultrafast consensus polishing of assemblies using mapped long (or short) reads. Use after long-read or hybrid assembly before binning/annotation. Upstream: https://github.com/lbcb-sci/racon.
デフォルトでは、最初にソースを確認する Prompt が選択されています。直接コマンドに切り替えるか、ローカルコピーをダウンロードすることもできます。
インストールを決める前に、SKILL.md と SkillsMP に表示されている付属ファイルをお読みください。
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
直接コマンドでは確認用 Prompt が省略されます。実行前にソースを確認してください。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill raconコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
ローカルで確認しますか？SkillsMP が現在取得できるファイルをダウンロードできます。
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.
SOC 職業分類に基づく
SKILL.md を表示中
| name | racon |
| description | Ultrafast consensus polishing of assemblies using mapped long (or short) reads. Use after long-read or hybrid assembly before binning/annotation. Upstream: https://github.com/lbcb-sci/racon. |
| license | MIT |
| category | analysis-tools |
| tags | ["polish","assembly","long-read"] |
| upstream | https://github.com/lbcb-sci/racon |
| stage | assembly |
Upstream: lbcb-sci/racon
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017). https://doi.org/10.1101/gr.214270.116
Racon polishes contigs given overlaps from mapping (usually Minimap2 PAF). Typical long-read loop: assemble → map reads → racon → (optional repeat). Do not expect Racon alone to fix massive mis-assemblies; it refines consensus.
For Illumina polishing of long-read drafts, consider pilon / Polypolish
ecosystems as alternatives.
conda install -c bioconda racon minimap2
minimap2 -x map-ont -t 16 assembly.fa reads.fastq.gz > temp/polish/map.paf
racon -t 16 reads.fastq.gz temp/polish/map.paf assembly.fa \
> temp/polish/assembly.racon.fa
minimap2 · metaflye · metamdbg · pilon · quast