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: github.com/CMU-SAFARI/FastRemap. Docker image available at: https://hub.docker.com/r/alkanlab/fastremap. Also available in Bioconda at: https://anaconda.org/bioconda/fastremap-bio.
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