FastRemap: a tool for quickly remapping reads between genome assemblies

Bioinformatics. 2022 Sep 30;38(19):4633-4635. doi: 10.1093/bioinformatics/btac554.


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.

Availability and implementation: FastRemap is written in C++. Source code and user manual are freely available at: Docker image available at: Also available in Bioconda at:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing* / methods
  • Sequence Analysis, DNA / methods
  • Software*