Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Level 7 Seminar Room 2, WEHI1

10 October 2017

Mapping of long sequence reads

Wei Shi
WEHI Bioinformatics

Third-generation sequencers, such as Oxford Nanopore sequencer, are becoming increasing popular in the genomic field. These sequencers generate significantly longer reads than the next-generation sequencers, for example the Nanopore MinION sequencer can produce reads of up to 1 million bases long. The availability of such reads makes it possible to address research questions that cannot be answered before. However, long reads are known to have a much higher sequencing error rate compared to short reads and this poses a significant challenge for applying the long-read sequencing technique in research and clinic.

Mapping of long reads to a reference genome is often the first step in the analysis of long reads generated in an experiment. Aligners designed for mapping short reads are unable to map long reads. A few recently developed long-read aligners were found to be extremely time consuming and have unsatisfactory performance in mapping accuracy. Here I describe a new long-read aligner called SubLong, which is based on the "seed-and-vote" paradigm which was designed for mapping both short and long reads. Using both real and simulation data, I will show that SubLong is much faster than popular long-read aligners and it also achieves a higher mapping accuracy.

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