modkit

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 • 1 shared operation

MethylDackel (formerly PileOMeth) -- fast C tool for extracting per-base methylation metrics from coordinate-sorted BAM/CRAM files produced by bisulfite sequencing aligners (Bismark, bwa-meth, BSMAP).

2 shared topics • 1 shared operation

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

Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner

2 shared topics

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

2 shared topics