Better quality score compression through sequence-based quality smoothing.

ABSTRACT:

Motivation

Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity of compression. Most of the entropy of NGS data lies in the quality values associated to each read. Those values are often more diversified than necessary. Because of that, many tools such as Quartz or GeneCodeq, try to change (smooth) quality scores in order to improve compressibility without altering the important information they carry for downstream analysis like SNP calling.

Results

We use the FM-Index, a type of compressed suffix array, to reduce the storage requirements of a dictionary of k-mers and an effective smoothing algorithm to maintain high prec

SUBMITTER: Shibuya Y 

PROVIDER: S-EPMC6873394 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature