bio-genome-assembly-scaffolding
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies.
npx skills add BioTender-max/awesome-bio-agent-skills --skill scaffolding --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+, QUAST 5.2+, bedtools 2.31+, 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 Scaffolding **"Scaffold my contigs to chromosome level"** → Order and orient contigs into chromosome-scale scaffolds using Hi-C proximity ligation data. - CLI: `yahs contigs.fa hic_alignments.bam`, `3d-dna`, `salsa2` ## Hi-C Data Preprocessing **Goal:** Prepare Hi-C read alignments for scaffolding tools. **Approach:** Align Hi-C reads with BWA mem using Hi-C-specific flags (-5SP), then filter and deduplicate contacts with pairtools. ```bash # Align Hi-C reads to draft assembly bwa index draft_assembly.fa bwa mem -5SP -t 16 draft_assembly.fa hic_R1.fq.gz hic_R2.fq.gz | \ samtools view -@ 8 -bhS - > aligned.bam # Filter for Hi-C contacts (pairtools) pairtools parse --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 \ --nproc-in 8 --nproc-out 8
- Version Compatibility
- Hi-C Data Preprocessing
- YaHS Scaffolding (Recommended)
- YaHS with Error Correction
- 3D-DNA Pipeline
- SALSA2 Scaffolding
- Generate Contact Map
- Visualize with HiGlass
- Manual Curation (Juicebox)
- Post-Scaffolding Gap Filling
- Validate Scaffolding
- Check Telomeres
- Rename to Chromosomes
- Related Skills
Align Hi-C reads to draft assembly bwa index draft_assembly.fa bwa mem -5SP -t 16 draft_assembly.fa hic_R1.fq.gz hic_R2.fq.gz | \ samtools view -@ 8 -bhS - > aligned.bam Filter for Hi-C contacts (pairtools) pairtools parse --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 \ pairtools sort --nproc 8 | \ pairtools dedup --nproc 8 --mark-dups | \ pairtools split --output-pairs contacts.pairs.gz Index assembly
What does the bio-genome-assembly-scaffolding skill do?
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill scaffolding --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.