bio-genome-assembly-hifi-assembly
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.
npx skills add BioTender-max/awesome-bio-agent-skills --skill hifi-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: BUSCO 5.5+, QUAST 5.2+ 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. # HiFi Assembly **"Assemble a genome from HiFi reads"** → Build a phased, reference-quality diploid assembly from PacBio HiFi reads with optional trio or Hi-C phasing for full haplotype resolution. - CLI: `hifiasm -o output reads.fq.gz` ## Basic Assembly **Goal:** Produce a primary contig assembly from PacBio HiFi reads. **Approach:** Run hifiasm with default parameters and convert GFA output to FASTA. ```bash # Primary assembly (single haplotype consensus) hifiasm -o output_prefix -t 32 reads.hifi.fastq.gz # Output files: # output_prefix.bp.p_ctg.gfa - Primary contigs # output_prefix.bp.a_ctg.gfa - Alternate contigs # output_prefix.bp.hap1.p_ctg.gfa - Haplotype 1 (if phased) # output_prefix.bp.hap2.p_ctg.gfa - Haplotype 2 (if
- Version Compatibility
- Basic Assembly
- Trio-Binned Phasing
- Hi-C Phasing
- Key Parameters
- Purge Duplicates
- Ultra-Long ONT Integration
- Assembly Stats
- Memory and Runtime
- Python Wrapper
- Troubleshooting
- Related Skills
Primary assembly (single haplotype consensus)
hifiasm -o output_prefix -t 32 reads.hifi.fastq.gz
Output files:
output_prefix.bp.p_ctg.gfa - Primary contigs
output_prefix.bp.a_ctg.gfa - Alternate contigs
output_prefix.bp.hap1.p_ctg.gfa - Haplotype 1 (if phased)
output_prefix.bp.hap2.p_ctg.gfa - Haplotype 2 (if phased)
Convert GFA to FASTA
awk '/^S/{print ">"$2;print $3}' output_prefix.bp.p_ctg.gfa > assembly.fasta
With parental short reads for trio binningWhat does the bio-genome-assembly-hifi-assembly skill do?
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill hifi-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.