Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

ABSTRACT:

Background

The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms.

Results

In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic

SUBMITTER: Caboche S 

PROVIDER: S-EPMC4051166 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature