LoRDEC: accurate and efficient long read error correction

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…

• AN
  Agence Nationale de la Recherche

  Awards: ANR-12-BS02-0008, ANR-12
• CN
  Centre National de la Recherche Scientifique