CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.

ABSTRACT: Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them with virtually elongated reads. However, due to the inherent limitations of most paired-end sequencers, the chance of observing erroneous bases grows rapidly as the end of a read is approached, which becomes a critical hurdle for accurately merging paired-end reads. Although there exist several sophisticated approaches to this problem, their performance in terms of quality of merging often remains unsatisfactory. To address this issue, here we present a context-aware scheme for paired-end reads (CASPER): a computational method to rapidly and robustly merge overlapping paired-end reads.

SUBMITTER: Kwon S 

PROVIDER: S-EPMC4168710 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature