BI
Literature
bio-longread-alignment
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Literature
BI
bio-methylation-bismark-alignment
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-methylation-bismark-alignment
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: bismark_genome_preparation genome/ then bismark --genome genome/ reads.fq.gz.
- 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.
- bismark_genome_preparation --bowtie2 /path/to/genome_folder/.
Source Doc
Excerpt From SKILL.md
Reduced Representation Bisulfite Sequencing
bismark --genome /path/to/genome_folder/
--pbat \ # For PBAT libraries (post-bisulfite adapter tagging)
reads.fastq.gz
Post-Bisulfite Adapter Tagging (e.g., scBS-seq)
bismark --genome /path/to/genome_folder/ --pbat reads.fastq.gz
## For libraries where all 4 strands are present
bismark --genome /path/to/genome_folder/ --non_directional reads.fastq.gz
Use cases
- Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
Not for
- Do not treat this catalog entry as a substitute for the full upstream workflow.
Upstream Related Skills
- methylation-calling - Extract methylation from Bismark BAM
- methylkit-analysis - Import Bismark output to R
- sequence-io/read-sequences - FASTQ handling
- alignment-files/sam-bam-basics - BAM manipulation
Related skills
Related skills
BI
Literature
bio-machine-learning-atlas-mapping
Map query cells to reference atlases with scANVI or Symphony.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Literature
bio-microbiome-taxonomy-assignment
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and ex…
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Literature
bio-phasing-imputation-reference-panels
Select and prepare reference panels (1KGP, HRC, TOPMed) for imputation.
FreedomIntelligence/OpenClaw-Medical-SkillsView