BSseeker2

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

3 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

3 shared topics • 1 shared operation

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

3 shared topics • 1 shared operation

nf-core/methylseq — community-curated Nextflow pipeline for whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data analysis. Handles adapter trimming (Tri

3 shared topics • 1 shared operation

dmrseq is an R/Bioconductor package for detecting differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) data. It fits a generalized least squares model with a smooth c

3 shared topics