Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing

Recently a number of programs have been proposed for mapping short reads to a reference genome. Many of them are heavily optimized for short-read mapping and hence are very efficient for shorter queries, but that makes them inefficient or not applicable for reads longer than 200bp. However, many sequencers are already generating longer reads and more are expected to follow. For long read sequence mapping, there are limited options; BLAT, SSAHA2, FANGS and BWA-SW are among the popular ones. However, re-sequencing and personalized medicine need much faster software to map these long sequencing reads to a reference genome to identify SNPs or rare transcripts

Provided by: Oxford University Press Topic: Software Date Added: Nov 2010 Format: PDF

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