FastRemap: a tool for quickly remapping reads between genome assemblies

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 7.82x speedup (6.47x, 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.

Automated summary

Motivation: A fast and efficient tool called FastRemap is introduced for remapping reads between genome assemblies. It provides a 7.82x speedup (6.47x on average) and consumes as low as 61.7% of peak memory compared to the state-of-the-art tool CrossMap.