| name | metagenomics-workflow |
| description | End-to-end shotgun metagenomics: quality control, assembly, mapping, binning, taxonomic annotation, functional annotation, microbial mining (BGCs, AMR, MGEs, element cycling, DOM, defense), and research analysis (stats/figures). Use when starting a project or ordering stages. For tool choice use tool-selection. For mining use microbial-mining; for paper stats use research-analysis. For public DBs use public-databases.
|
| license | MIT |
| category | orchestration |
| tags | ["guidance","pipeline","workflow","QC","assembly","mapping","binning","taxonomy","function","mining","research-analysis"] |
Metagenomics Workflow
Organize by scientific stage. Mapping sits between assembly and binning.
Microbial mining is an optional discovery track on contigs/MAGs.
Path
study-design + setup (+ public-databases)
│
v
1 QC fastp → kneaddata
│
├─► 5 taxonomy / 6 function (reads) ─► research-analysis
│
v
2 Assembly megahit | metaspades | metaflye | metamdbg
(± binchicken for targeted coassembly)
│
v
3 Mapping strobealign | bowtie2 | bwa-mem2 | minimap2 → samtools
│
├─► 6 function (genes)
│
v
4 Binning single binners → basalt ★ | metawrap | dastool
→ (± anvio refine | deepurify clean)
→ drep → coverm → checkm2 / gunc / mag-qc
│
├─► 5 taxonomy (genomes): gtdbtk
├─► 6 function (genomes): bakta / prokka / eggnog-mapper / rgi
└─► 7 microbial mining: antismash / genomad→checkv→vcontact / dram / …
│
v
research-analysis (multiqc · microeco · maaslin2 · …) → Methods archive
Common paths
| Goal | Route |
|---|
| Composition only | QC → metaphlan / singlem / kraken2 → research-analysis |
| Genome-resolved catalogue | QC → assembly → mapping → basalt ★ → mag-qc → gtdbtk |
| Interactive MAG polish | After auto-bins → anvio → re-QC |
| Environmental unknowns | QC → singlem (± binchicken coassembly) |
| Viral ecology | contigs → genomad/virsorter2 → checkv → vcontact |
Checklist
Related skills
tool-selection · research-analysis · microbial-mining · homology-search ·
phylogenomics · metagenomics-llm · public-databases · study-design ·
mag-qc · stage skills under skills/
