BCmet

BCmet is a command-line tool designed for processing sequencing data. It is part of the BCBio package, a popular open-source platform for bioinformatics analysis. BCmet's primary function is to handle methylation data generated from bisulfite sequencing experiments. This type of sequencing is used to study DNA methylation, a crucial epigenetic modification that plays a role in gene regulation and cellular processes.

The tool takes raw sequencing reads as input and aligns them to a reference genome. During the alignment process, BCmet specifically accounts for the characteristic changes in DNA bases that occur after bisulfite treatment. Following alignment, it quantifies methylation levels at individual cytosine sites across the genome. This quantification typically involves determining the proportion of reads that show a methylated versus unmethylated cytosine at each position.

BCmet can output methylation calls in various formats, making it compatible with downstream analysis tools. These outputs often include information about the specific cytosine context (e.g., CpG, CHG, CHH) and the number of methylated and unmethylated reads supporting each call. This detailed information allows researchers to investigate patterns of DNA methylation, identify differentially methylated regions, and explore their relationship with gene expression or other biological phenomena. Its integration within the BCBio framework simplifies the pipeline for performing comprehensive bisulfite sequencing analysis.