Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing

Abstract

Abstract Summary In whole genome sequencing data, polymerase chain reaction amplification results in duplicate DNA fragments coming from the same location in the genome. The process of preparing a whole genome bisulfite sequencing (WGBS) library, on the other hand, can create two DNA fragments from the same location that should not be considered duplicates. Currently, only one WGBS-aware duplicate marking tool exists. However, it only works with the output from a single tool, does not accept streaming input or output, and requires a substantial amount of memory relative to the input size. Dupsifter provides an aligner-agnostic duplicate marking tool that is lightweight, has streaming capabilities, and is memory efficient. Availability and implementation Source code and binaries are freely available at https://github.com/huishenlab/dupsifter under the MIT license. Dupsifter is implemented in C and is supported on macOS and Linux.