Repository: Freie Universit├Ąt Berlin, Math Department

RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data

Hetzel, Sara and Giesselmann, Pay and Reinert, Knut and Meissner, Alexander and Kretzmer, Helene and Alkan, Can (2021) RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinformatics, 37 (21). pp. 3934-3935. ISSN 1367-4803

Full text not available from this repository.

Official URL: https://doi.org/10.1093/bioinformatics/btab663

Abstract

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

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:2698
Deposited By: Anja Kasseckert
Deposited On:02 Feb 2022 13:58
Last Modified:02 Feb 2022 13:58

Repository Staff Only: item control page