Data-dependent bucketing improves reference-free compression of sequencing reads.

ABSTRACT:

Motivation

The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data.

Results

We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in fil

SUBMITTER: Patro R 

PROVIDER: S-EPMC4547610 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature