BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.

ABSTRACT:

Background

Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition,

SUBMITTER: Eagles NJ 

PROVIDER: S-EPMC10498615 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature