bio-read-alignment-bowtie2-alignment
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bowtie2-alignment --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: 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. # Bowtie2 Alignment **"Align DNA reads with Bowtie2"** → Map short reads to a reference genome using Bowtie2's end-to-end or local alignment modes. - CLI: `bowtie2 -x index -1 R1.fq -2 R2.fq | samtools sort -o aligned.bam` ## Build Index ```bash # Build index from reference FASTA bowtie2-build reference.fa reference_index # With threads (faster) bowtie2-build --threads 8 reference.fa reference_index # Creates: reference_index.1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 ``` ## Basic Alignment ```bash # Paired-end reads bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz -S aligned.sam # Single-end reads bowtie2 -p 8 -x reference_index -U reads.fq.gz -S aligned.sam # Direct to sorted BAM bowtie2 -p 8 -x reference_index -1 r1.fq.gz -2 r2.fq.gz | \ samtools sort -@ 4 -o aligned.sorted.bam - ``
- Version Compatibility
- Build Index
- Basic Alignment
- Alignment Modes
- Sensitivity Presets
- ChIP-seq Alignment
- ATAC-seq Alignment
- Fragment Size Options
- Read Group and Output Options
- Multi-mapping Reads
- Output Unmapped Reads
- Key Parameters
- Alignment Statistics
- Related Skills
Build index from reference FASTA bowtie2-build reference.fa reference_index With threads (faster) bowtie2-build --threads 8 reference.fa reference_index Paired-end reads bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz -S aligned.sam Single-end reads bowtie2 -p 8 -x reference_index -U reads.fq.gz -S aligned.sam Direct to sorted BAM bowtie2 -p 8 -x reference_index -1 r1.fq.gz -2 r2.fq.gz | \
What does the bio-read-alignment-bowtie2-alignment skill do?
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bowtie2-alignment --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.