bio-genome-assembly-metagenome-assembly
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.
npx skills add BioTender-max/awesome-bio-agent-skills --skill metagenome-assembly --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: QUAST 5.2+, SPAdes 3.15+, minimap2 2.26+, pandas 2.2+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metagenome Assembly **"Assemble genomes from my metagenome data"** → Reconstruct individual microbial genomes (MAGs) from mixed community sequencing reads using metagenome-aware assemblers and binning. - CLI: `flye --meta --nano-raw reads.fq` (long-read), `metaspades.py -1 R1.fq -2 R2.fq` (short-read) ## Overview Metagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circular genomes and resolution of strain-level differences. ## metaFlye (Long Reads) **Goal:** Assemble metagenome contigs from long reads handling uneven coverage across species. **Approach:** Run Flye in --meta mode which accounts for varying coverage dep
- Version Compatibility
- Overview
- metaFlye (Long Reads)
- metaSPAdes (Short Reads)
- Hybrid Assembly
- Key Parameters
- metaFlye
- metaSPAdes
- Binning Workflow
- SemiBin2 (Deep Learning Binning)
- Quality Assessment
- Circular Genome Detection
- Python Pipeline
- Expected Outputs
ONT metagenome assembly flye --nano-raw reads.fastq.gz \ PacBio HiFi metagenome flye --pacbio-hifi reads.hifi.fastq.gz \ Key output files: assembly.fasta - assembled contigs assembly_graph.gfa - assembly graph assembly_info.txt - contig statistics Illumina paired-end metagenome metaspades.py -1 R1.fastq.gz -2 R2.fastq.gz \
What does the bio-genome-assembly-metagenome-assembly skill do?
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill metagenome-assembly --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.