Coordinate binning, refinement, and QC to construct high-quality MAGs.
npx skills add https://github.com/fmschulz/omics-skills --skill bio-binning-qc
Please help me install this Agent Skill. Skill: bio-binning-qc Source: https://github.com/fmschulz/omics-skills/tree/main/skills/bio-binning-qc Command: npx skills add https://github.com/fmschulz/omics-skills --skill bio-binning-qc
Bins derived from metagenomic data often require manual curation and multi-tool QC to meet publication-ready quality. This Skill coordinates automated binning, refinement, and risk-based QC gating to produce high-quality MAGs with transparent criteria.
Run the workflow on your contig assemblies to generate MAG bins and pass QC gates before downstream analyses.
High-intent search queries and answers about installing and using this skill.
Automated MAG binning pipelines coordinate binning, refinement, and quality control to generate high-quality metagenome-assembled genomes. This Skill orchestrates multiple binners and applies domain-aware QC gates to produce publication-ready MAGs with transparent metrics.
Checking MAGs for contamination and chimerism involves applying domain-specific quality control tools like CheckM2 and GUNC. This Skill enforces QC gates using these tools to filter high-quality bins and ensure recovery purity for downstream analysis.
Yes, you can use CheckM2 and EukCC together for prokaryotic and eukaryotic bin QC. This Skill applies domain-aware quality control, running CheckM2 for bacteria and archaea while using EukCC specifically for eukaryotic bins to validate quality.
Refining metagenomic bins from MetaBAT2 and SemiBin2 involves multi-binner coordination to maximize recovery and purity. This Skill runs and optionally refines bins generated by these tools to produce clearly organized, high-quality MAGs.
Automated binning refinement limitations depend on input assembly quality and the ability of binning tools to resolve closely related strains. This Skill validates inputs and enforces QC gates, but complex microbial communities may still require manual curation to meet publication-ready standards.
nahisahoReconstruct metagenome-assembled genomes from metagenomic data with binning, quality assessment, taxonomy, dereplication, and annotation.
MDheweiAnnotate ATAC-seq or ChIP-seq peaks with genomic context and QC metrics.
rhysnewellAutomate metagenomic assembly, binning, annotation, and dereplication workflows.
Sheldon-92Enforce contamination checks, deduplication, and quality filtering on synthetic datasets.
