bwa-meth

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

Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner

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

Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.

2 shared topics • 2 shared operations