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BI
bio-genome-assembly-short-read-assembly
Maintainer FreedomIntelligence · Last updated April 1, 2026
Illumina de novo assembly with SPAdes for metagenomes/bacteria/transcriptomes.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-short-read-assembly
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Assemble genomes from Illumina paired-end or single-end reads using SPAdes.
- spades.py \ -1 illumina_R1.fq.gz -2 illumina_R2.fq.gz \ --nanopore nanopore.fq.gz \ -o hybrid_assembly.
Source Doc
Excerpt From SKILL.md
SPAdes Overview
SPAdes (St. Petersburg genome Assembler) uses de Bruijn graph approach with multiple k-mer sizes for robust assembly.
Isolate Mode (Default for Bacteria)
Best for single-organism isolates with uniform coverage.
Careful Mode
Reduces misassemblies at cost of speed. Recommended for small genomes.
Use cases
- Use bio-genome-assembly-short-read-assembly for genomics and bioinformatics workflows.
- Apply bio-genome-assembly-short-read-assembly to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- read-qc - Preprocess reads before assembly
- assembly-polishing - Polish assembly with Pilon
- assembly-qc - Assess with QUAST/BUSCO
- long-read-assembly - Long-read alternatives
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