Fast and accurate read alignment for resequencing.

ABSTRACT:

Motivation

Next-generation sequence analysis has become an important task both in laboratory and clinical settings. A key stage in the majority sequence analysis workflows, such as resequencing, is the alignment of genomic reads to a reference genome. The accurate alignment of reads with large indels is a computationally challenging task for researchers.

Results

We introduce SeqAlto as a new algorithm for read alignment. For reads longer than or equal to 100 bp, SeqAlto is up to 10 × faster than existing algorithms, while retaining high accuracy and the ability to align reads with large (up to 50 bp) indels. This improvement in efficiency is particularly important in the analysis of future sequencing data where the number of reads approaches many billions. Furthermore, SeqAl

SUBMITTER: Mu JC 

PROVIDER: S-EPMC3436849 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature