FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies

TL;DR

FastRemap is a new tool that significantly accelerates genome read remapping between assemblies, reducing computational time and memory usage compared to existing solutions, thus facilitating large-scale genomic analyses.

Contribution

FastRemap introduces a high-performance, memory-efficient tool for remapping reads between genome assemblies, outperforming existing methods in speed and resource consumption.

Findings

Up to 7.82× faster than CrossMap

Uses as low as 61.7% of peak memory of CrossMap

Average speedup of 6.47× across tests

Abstract

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.