EpiDISH

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

1 shared topic • 1 shared operation

Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner

1 shared topic • 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

1 shared topic • 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

1 shared topic • 1 shared operation

wigToBigWig converts Wiggle (.wig) format files — fixedStep and variableStep — to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-s

1 shared topic • 1 shared operation