FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Year: 2022
Type: dataset
Abstract: A genome read data set can be quickly and eciently 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 ecient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.19× speedup (5.97×, 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++. Source code and user manual are freely available at: github.com/CMU-SAFARI/FastRemap
Institutions: ETH Zurich, Carnegie Mellon University, Bilkent University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4393567825