bio-workflows-genome-assembly-pipeline
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.
npx skills add BioTender-max/awesome-bio-agent-skills --skill genome-assembly-pipeline --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: BUSCO 5.5+, BWA 0.7.17+, Flye 2.9+, QUAST 5.2+, SPAdes 3.15+, fastp 0.23+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - 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. # Genome Assembly Pipeline **"Assemble and polish a genome from my sequencing reads"** → Orchestrate read QC, assembly (hifiasm, Flye, SPAdes), polishing (Medaka, Pilon), scaffolding, contamination detection (BlobToolKit), and quality assessment (QUAST, BUSCO). Complete workflow from sequencing reads to polished, quality-assessed genome assembly. ## Workflow Overview ``` Reads (short and/or long) | v [1. QC & Filtering] -----> fastp, NanoPlot | v [2. Assembly] -----------> SPAdes (short) or Flye (long) | v [3. Polishing] ----------> Pilon (short) or medaka (long) | v [4. QC Assessment] ------> QUAST, BUSCO | v Final polished assembly ``` ## Path A: Short-Read Assembly (SPAdes) ### Step 1: QC ```bash fastp -i reads_R1.fastq.gz -I reads_R2.f
- Version Compatibility
- Workflow Overview
- Path A: Short-Read Assembly (SPAdes)
- Step 1: QC
- Step 2: Assembly with SPAdes
- Step 3: Polishing with Pilon
- Path B: Long-Read Assembly (Flye)
- Step 2: Assembly with Flye
- Step 3: Polishing with medaka
- Path C: Hybrid Assembly
- Step 4: Quality Assessment
- QUAST
- BUSCO
- Parameter Recommendations
fastp -i reads_R1.fastq.gz -I reads_R2.fastq.gz \ Standard bacterial assembly spades.py \ For isolate genomes spades.py --isolate \ Align reads to assembly bwa index spades_output/scaffolds.fasta bwa mem -t 16 spades_output/scaffolds.fasta \ trimmed_R1.fq.gz trimmed_R2.fq.gz | \ samtools sort -@ 4 -o aligned.bam
What does the bio-workflows-genome-assembly-pipeline skill do?
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill genome-assembly-pipeline --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.