bio-genome-assembly-short-read-assembly
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.
npx skills add BioTender-max/awesome-bio-agent-skills --skill short-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: FastQC 0.12+, MEGAHIT 1.2+, SPAdes 3.15+ 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. # Short-Read Assembly **"Assemble a genome from Illumina reads"** → Build a de novo assembly from short paired-end reads using de Bruijn graph algorithms with multiple k-mer sizes. - CLI: `spades.py -1 R1.fq.gz -2 R2.fq.gz -o output` ## SPAdes Overview SPAdes (St. Petersburg genome Assembler) uses de Bruijn graph approach with multiple k-mer sizes for robust assembly. ### Installation ```bash conda install -c bioconda spades ``` ## Basic Usage ### Paired-End Assembly ```bash spades.py -1 R1.fastq.gz -2 R2.fastq.gz -o output_dir ``` ### Single-End Assembly ```bash spades.py -s reads.fastq.gz -o output_dir ``` ### With Unpaired Reads ```bash spades.py -1 R1.fastq.gz -2 R2.fastq.gz -s unpaired.fastq.gz -o output_dir ``` ## Assembly Modes ### Isolate Mode (Default for Bacteria) ```bash spade
- Version Compatibility
- SPAdes Overview
- Installation
- Basic Usage
- Paired-End Assembly
- Single-End Assembly
- With Unpaired Reads
- Assembly Modes
- Isolate Mode (Default for Bacteria)
- Careful Mode
- Meta Mode (Metagenomes)
- RNA Mode (Transcriptomes)
- Plasmid Mode
- Key Options
conda install -c bioconda spades spades.py -1 R1.fastq.gz -2 R2.fastq.gz -o output_dir spades.py -s reads.fastq.gz -o output_dir spades.py -1 R1.fastq.gz -2 R2.fastq.gz -s unpaired.fastq.gz -o output_dir spades.py --isolate -1 R1.fq.gz -2 R2.fq.gz -o isolate_assembly spades.py --careful -1 R1.fq.gz -2 R2.fq.gz -o careful_assembly spades.py --meta -1 R1.fq.gz -2 R2.fq.gz -o meta_assembly spades.py --rna -1 R1.fq.gz -2 R2.fq.gz -o rna_assembly spades.py --plasmid -1 R1.fq.gz -2 R2.fq.gz -o plasmid_assembly spades.py \
What does the bio-genome-assembly-short-read-assembly skill do?
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill short-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.