RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data.

ABSTRACT:

 

Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various informative metrics have been established to explore this information. However, limited compatibility with alignment tools, reference genomes or the measurements they provide present a bottleneck for most groups to include this information as standard analysis. To address this, we developed RLM, a fast and scalable tool for the computation of frequently used Read-Level Methylation statistics. RLM supports several common alignment tools, works independently of the reference genome and handles all frequently used sequencing experiment designs. RLM can process large input files with a billion reads in just a few hours on common workstations.

Availability

https://github.com/sarahet/RLM.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Hetzel S 

PROVIDER: S-EPMC8686677 | biostudies-literature |

REPOSITORIES: biostudies-literature