bio-read-alignment-bwa-alignment
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bwa-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: GATK 4.5+, 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. # BWA-MEM2 Alignment **"Align reads with BWA"** → Map DNA reads to a reference genome using BWA-MEM2, the standard aligner for whole-genome and exome sequencing. - CLI: `bwa-mem2 mem -t 8 ref.fa R1.fq R2.fq | samtools sort -o aligned.bam` ## Build Index ```bash # Index reference genome (required once) bwa-mem2 index reference.fa # Creates: reference.fa.0123, reference.fa.amb, reference.fa.ann, reference.fa.bwt.2bit.64, reference.fa.pac ``` ## Basic Alignment ```bash # Paired-end reads bwa-mem2 mem -t 8 reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam # Single-end reads bwa-mem2 mem -t 8 reference.fa reads.fq.gz > aligned.sam ``` ## Alignment with Read Groups ```bash # Add read group information (required for GATK) bwa-mem2 mem -t 8 \ -R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA\tLB:lib1' \ refere
- Version Compatibility
- Build Index
- Basic Alignment
- Alignment with Read Groups
- Direct to Sorted BAM
- Mark Duplicates Pipeline
- Common Options
- Key Parameters
- Output Filters
- Split Read Alignment
- Memory Requirements
- BWA-MEM (Alternative)
- BWA-MEM vs BWA-MEM2
- Related Skills
Index reference genome (required once) bwa-mem2 index reference.fa Paired-end reads bwa-mem2 mem -t 8 reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam Single-end reads bwa-mem2 mem -t 8 reference.fa reads.fq.gz > aligned.sam Add read group information (required for GATK) bwa-mem2 mem -t 8 \ reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam Pipe to samtools for sorted BAM output
What does the bio-read-alignment-bwa-alignment skill do?
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bwa-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.