HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads.

ABSTRACT:

Background and objective

Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data.

Methods

We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read l

SUBMITTER: Li P 

PROVIDER: S-EPMC3932469 | biostudies-literature | 2014 Mar-Apr

REPOSITORIES: biostudies-literature