Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.

ABSTRACT:

Background

Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome RNA/cDNA sequencing, where fragments shorter than a read are sometimes obtained because of the limitations of NGS protocols. For the newly emerged Nextera long mate-pair (LMP) protocol, junction adapters are located in the middle of all properly constructed fragments; hence, adapter trimming is essential to gain the correct paired reads. However, our investigations have shown that few adapter trimming tools meet both efficiency and accuracy requirements simultaneousl

SUBMITTER: Jiang H 

PROVIDER: S-EPMC4074385 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature