Bioinformatics Seminar
Time:
Venue: Na
10 October 2017
NaMapping of long sequence reads
Wei ShiWEHI 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.;;