LoRDEC: accurate and efficient long read error correction.

ABSTRACT:

Motivation

PacBio single molecule real-time sequencing is a third-generation sequencing technique producing long reads, with comparatively lower throughput and higher error rate. Errors include numerous indels and complicate downstream analysis like mapping or de novo assembly. A hybrid strategy that takes advantage of the high accuracy of second-generation short reads has been proposed for correcting long reads. Mapping of short reads on long reads provides sufficient coverage to eliminate up to 99% of errors, however, at the expense of prohibitive running times and considerable amounts of disk and memory space.

Results

We present LoRDEC, a hybrid error correction method that builds a succinct de Bruijn graph representing the short reads, and seeks a corrective sequence for

SUBMITTER: Salmela L 

PROVIDER: S-EPMC4253826 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature