RT Journal Article
SR Electronic
T1 Featherweight long read alignment using partitioned reference indexes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 386847
DO 10.1101/386847
A1 Hasindu Gamaarachchi
A1 Sri Parameswaran
A1 Martin A. Smith
YR 2018
UL http://biorxiv.org/content/early/2018/08/07/386847.abstract
AB 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.