bio-genome-assembly-long-read-assembly
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.
npx skills add BioTender-max/awesome-bio-agent-skills --skill long-read-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: Canu 2.2+, Flye 2.9+, hifiasm 0.19+, wtdbg2 2.5+ 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. # Long-Read Assembly **"Assemble a genome from long reads"** → Build a contiguous de novo assembly from ONT or PacBio reads, producing complete or near-complete chromosomes. - CLI: `flye --nano-raw reads.fq -o output` (ONT), `canu -p asm -d output -nanopore reads.fq` (ONT/PacBio) ## Tool Comparison | Tool | Speed | Memory | Best For | |------|-------|--------|----------| | Flye | Fast | Moderate | General purpose, bacteria, ONT | | Canu | Slow | High | High accuracy, complex genomes | | Wtdbg2 | Very fast | Low | Draft assemblies | > **Note:** For PacBio HiFi data, see the dedicated **hifi-assembly** skill which covers hifiasm. ## Flye ### Installation ```bash conda install -c bioconda flye ``` ### Basic Usage ```bash # Oxford Nanopore flye --nano-raw reads.fastq.gz --out-dir fly
- Version Compatibility
- Tool Comparison
- Flye
- Installation
- Basic Usage
- Read Type Options
- Key Options
- Genome Size Estimation
- Output Files
- Bacterial Assembly
- Metagenome Assembly
- With Plasmid Recovery
- Canu
- Fast Mode
conda install -c bioconda flye Oxford Nanopore flye --nano-raw reads.fastq.gz --out-dir flye_output --threads 16 PacBio CLR flye --pacbio-raw reads.fastq.gz --out-dir flye_output --threads 16 PacBio HiFi flye --pacbio-hifi reads.fastq.gz --out-dir flye_output --threads 16 Estimate if unknown flye --nano-raw reads.fq.gz --out-dir output --genome-size 5m Size formats: 1000, 1k, 1m, 1g
What does the bio-genome-assembly-long-read-assembly skill do?
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill long-read-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.