Improving read mapping using additional prefix grams.

ABSTRACT:

Background

Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie and BWA, are optimized to return top one or a few candidate locations of each read. However, identifying all mapping locations of each read, instead of just one or a few, is also important in some sequencing applications such as ChIP-seq for discovering binding sites in repeat regions, and RNA-seq for transcript abundance estimation.

Results

Here we present Hobbes2, a software package designed for fast and accurate alignment of NGS reads and specialized in identifying all mapping locations of

SUBMITTER: Kim J 

PROVIDER: S-EPMC3927682 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature