bio-methylation-bismark-alignment
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bismark-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: Bowtie2 2.5.3+, HISAT2 2.2.1+, Trim Galore 0.6.10+, 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. # Bismark Alignment **"Align my bisulfite sequencing reads"** → Map WGBS/RRBS reads to an in-silico bisulfite-converted reference genome, producing BAM files with methylation context tags. - CLI: `bismark_genome_preparation genome/` then `bismark --genome genome/ reads.fq.gz` ## Prepare Genome Index ```bash # One-time genome preparation (creates bisulfite-converted index) bismark_genome_preparation --bowtie2 /path/to/genome_folder/ # Genome folder should contain FASTA files (e.g., hg38.fa, chr1.fa, etc.) # Creates Bisulfite_Genome/ subdirectory with CT and GA converted indices ``` ## Basic Single-End Alignment ```bash bismark --genome /path/to/genome_folder/ reads.fastq.gz -o output_dir/ ``` ## Paired-End Alignment ```bash bismark --genome /path/to/genome_folder
- Version Compatibility
- Prepare Genome Index
- Basic Single-End Alignment
- Paired-End Alignment
- Common Options
- RRBS Mode
- PBAT Libraries
- Non-Directional Libraries
- With Quality/Adapter Trimming (Pre-alignment)
- Multicore Processing
- Output Files
- Sort and Index BAM
- Deduplicate (Optional)
- Check Alignment Statistics
One-time genome preparation (creates bisulfite-converted index) bismark_genome_preparation --bowtie2 /path/to/genome_folder/ Genome folder should contain FASTA files (e.g., hg38.fa, chr1.fa, etc.) Creates Bisulfite_Genome/ subdirectory with CT and GA converted indices bismark --genome /path/to/genome_folder/ reads.fastq.gz -o output_dir/ bismark --genome /path/to/genome_folder/ \ reads.fastq.gz Reduced Representation Bisulfite Sequencing MspI digestion (RRBS standard) Bismark handles MspI-digested libraries automatically
What does the bio-methylation-bismark-alignment skill do?
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bismark-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.