Featherweight long read alignment using partitioned reference indexes release_r7aowocki5glvlc2d2jhep7g6y

by Hasindu Gamaarachchi, Sri Parameswaran, Martin Smith

Released as a post by Cold Spring Harbor Laboratory.

2018  

Abstract

The advent of nanopore sequencing has realised portable genomic research and applications. However, state of the art long read aligners and large reference genomes are not compatible with most mobile computing devices due to their high memory requirements. We show how memory requirements can be reduced through parameter optimization and reference genome partitioning, but highlight the associated limitations and caveats of these approaches. We then demonstrate how these issues can be overcome through an appropriate merging technique. We extend the Minimap2 aligner and demonstrate that long read alignment to the human genome can be performed on a system with 2GB RAM with negligible impact on accuracy.
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Date   2018-08-07
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