Reference-based compression of short-read sequences using path encoding.

ABSTRACT:

Motivation

Storing, transmitting and archiving data produced by next-generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed.

Results

We present here an approach to compression that reduces the difficulty of managing large-scale sequencing data. Our novel approach sits between pure reference-based compression and reference-free compression and combines much of the benefit of reference-based approaches with the flexibility of de novo encoding. Our method, called path encoding, draws a connection between storing paths in de Bruijn graphs and context-dependent arithmetic coding. Supporting this method is a system to compactly store sets of kmers that is of independent interest. We are able to encode

SUBMITTER: Kingsford C 

PROVIDER: S-EPMC4481695 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature