BitMapper: an efficient all-mapper based on bit-vector computing.

ABSTRACT:

Background

As the next-generation sequencing (NGS) technologies producing hundreds of millions of reads every day, a tremendous computational challenge is to map NGS reads to a given reference genome efficiently. However, existing methods of all-mappers, which aim at finding all mapping locations of each read, are very time consuming. The majority of existing all-mappers consist of 2 main parts, filtration and verification. This work significantly reduces verification time, which is the dominant part of the running time.

Results

An efficient all-mapper, BitMapper, is developed based on a new vectorized bit-vector algorithm, which simultaneously calculates the edit distance of one read to multiple locations in a given reference genome. Experimental results on both simulated a

SUBMITTER: Cheng H 

PROVIDER: S-EPMC4462005 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature