  A genome read data set 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 data sets and references,
high-performance remapping tools will be even more important for keeping up
with the computational demands of genome assembly and analysis.
  We provide FastRemap, a fast and efficient tool for remapping reads between
genome 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 the
peak memory consumption compared to the state-of-the-art remapping tool,
CrossMap.
  FastRemap is written in C++. The source code and user manual are freely
available 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.
