K-mer Counting for Genomic Big Data

Abstract

Counting the abundance of all the k-mers (substrings of length k) in sequencing reads is an important step of many bioinformatics applications, including de novo assembly, error correction and multiple sequence alignment. However, processing large amount of genomic dataset (TB range) has become a bottle neck in these bioinformatics pipelines. At present, most of the k-mer counting tools are based on single node, and cannot handle the data at TB level efficiently. In this paper, we propose a new distributed method for k-mer counting with high scalability. We test our k-mer counting tool on Mira supercomputer at Argonne National Lab, the experimental results show that it can scale to 8192 cores with an efficiency of 43% when processing 2 TB simulated genome dataset with 200 billion distinct k-mers (graph size), and only 578 s is used for the whole genome statistical analysis.