HIA: a genome mapper using hybrid index-based sequence alignment.

ABSTRACT:

Background

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools.

Results

HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table

SUBMITTER: Choi J 

PROVIDER: S-EPMC4688996 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature