BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis.

ABSTRACT:

Motivation

High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times.

Method

BioSeqZip generates compact and sorted lists of alignment-ready non-redundant sequences, keeping track of their occurrences in the raw files as well as of their quality score information. By exploiting a memory-co

SUBMITTER: Urgese G 

PROVIDER: S-EPMC7203750 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature