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A genome read data set can be quickly and efficiently remapped from onereference to another similar reference (e.g., between two reference versions ortwo similar species) using a variety of tools, e.g., the commonly-used CrossMaptool. With the explosion of available genomic data sets and references,high-performance remapping tools will be even more important for keeping upwith the computational demands of genome assembly and analysis.  We provide FastRemap, a fast and efficient tool for remapping reads betweengenome assemblies. FastRemap provides up to a 7.82$\times$ speedup(6.47$\times$, on average) and uses as low as 61.7% (80.7%, on average) of thepeak memory consumption compared to the state-of-the-art remapping tool,CrossMap.  FastRemap is written in C++. The source code and user manual are freelyavailable at: github.com/CMU-SAFARI/FastRemap. Docker image available at:https://hub.docker.com/r/alkanlab/fast. Also available in Bioconda at:https://anaconda.org/bioconda/fastremap-bio.

FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies