MethylDackel -- Methylation Extraction from BAM/CRAM Files

Fastq Screen — Perl tool for screening FASTQ sequencing reads against multiple reference genomes to detect sample contamination. Maps reads to user-defined genome databases (human, mouse, E. coli, Phi

2 shared topics • 2 shared operations

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

2 shared topics • 1 shared operation

Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner

2 shared topics • 1 shared operation

bwa-meth -- fast and accurate bisulfite-seq (WGBS/RRBS) aligner built on BWA-MEM. Performs in-silico C-to-T conversion of reads and reference, aligns with BWA-MEM or BWA-MEM2, and recovers original ba

2 shared topics • 1 shared operation

Use this skill for GATK-based DNA methylation and bisulfite sequencing workflows including WGBS preprocessing, base quality score recalibration for bisulfite data, duplicate marking of bisulfite reads

2 shared topics • 1 shared operation