Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers

Abstract

Summary: Removing duplicate and near-duplicate reads, generated by high-throughput sequencing technologies, is able to reduce computational resources in downstream applications. Here we develop minirmd, a de novo tool to remove duplicate reads via multiple rounds of clustering using different length of minimizer. Experiments demonstrate that minirmd removes more near-duplicate reads than existing clustering approaches and is faster than existing multi-core tools. To the best of our knowledge, minirmd is the first tool to remove near-duplicates on reverse-complementary strand.

Availability and implementation: https://github.com/yuansliu/minirmd.

Supplementary information: Supplementary data are available at Bioinformatics online.