FastRemap: a tool for quickly remapping reads between genome assemblies

Abstract

Motivation: A genome read dataset can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly used CrossMap tool. With the explosion of available genomic datasets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis. Results: We provide FastRemap, a fast and efficient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.82 speedup (6.47, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap.