bio-read-alignment-hisat2-alignment
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
npx skills add majiayu000/claude-skill-registry --skill hisat2-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.
# HISAT2 RNA-seq Alignment ## Build Index ```bash # Basic index (no annotation) hisat2-build -p 8 reference.fa hisat2_index # Index with splice sites and exons (recommended) hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt hisat2_extract_exons.py annotation.gtf > exons.txt hisat2-build -p 8 \ --ss splice_sites.txt \ --exon exons.txt \ reference.fa hisat2_index ``` ## Basic Alignment ```bash # Paired-end reads hisat2 -p 8 -x hisat2_index \ -1 reads_1.fq.gz -2 reads_2.fq.gz \ -S aligned.sam # Single-end reads hisat2 -p 8 -x hisat2_index \ -U reads.fq.gz \ -S aligned.sam ``` ## Direct to Sorted BAM ```bash # Pipe to samtools hisat2 -p 8 -x hisat2_index \ -1 r1.fq.gz -2 r2.fq.gz | \ samtools sort -@ 4 -o aligned.sorted.bam - samtools index aligned.sorted.bam ``` ## Stranded Libraries ```bash # Forward stranded (e.g., Ligation) hisat2 -p 8 -x hisat2_index \ --rna-strandness FR \ -1 r1.fq.gz -2 r2.fq.gz -S aligned.sam # Reverse stranded (e.g., dUTP, TruSeq - most common) hisat2 -p 8 -x hisat2_index \ --rna-strandness RF \ -1 r1.fq.gz -2 r2.fq.gz -S aligned.sam # Single-end stranded hisat2 -p 8 -x hisat2_index \ --rna-strandness F \ # or R for reverse -U reads.fq.gz -S ali
- Build Index
- Basic Alignment
- Direct to Sorted BAM
- Stranded Libraries
- Novel Splice Junction Discovery
- Two-Pass Alignment (Manual)
- Read Group Information
- Downstream Quantification
- Key Parameters
- For StringTie/Cufflinks
- Alignment Summary
- Memory Comparison
- Related Skills
Basic index (no annotation) hisat2-build -p 8 reference.fa hisat2_index Index with splice sites and exons (recommended) hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt hisat2_extract_exons.py annotation.gtf > exons.txt hisat2-build -p 8 \ reference.fa hisat2_index Paired-end reads hisat2 -p 8 -x hisat2_index \ Single-end reads
What does the bio-read-alignment-hisat2-alignment skill do?
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill hisat2-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 majiayu000/claude-skill-registry, a repository with 534 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.