Department of Computer Engineering, ETH Zurich, D-ITET, Zurich 8006, Switzerland.
Department of Computer Engineering, Bionano Genomics, San Diego, CA 92121, USA.
Bioinformatics. 2022 Sep 30;38(19):4633-4635. doi: 10.1093/bioinformatics/btac554.
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.
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.
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.
使用各种工具，例如常用的 CrossMap 工具，可以快速有效地将基因组读取数据集从一个参考基因组重新映射到另一个类似的参考基因组（例如，在两个参考版本或两个相似物种之间）。随着可用基因组数据集和参考基因组的爆炸式增长，高性能的重新映射工具对于满足基因组组装和分析的计算需求将变得更加重要。
我们提供了 FastRemap，这是一种用于在基因组组装之间重新映射读取的快速高效工具。FastRemap 提供了高达 7.82 倍的加速（平均 6.47 倍），与最先进的重新映射工具 CrossMap 相比，仅使用 61.7%（平均 80.7%）的峰值内存消耗。
FastRemap 是用 C++编写的。源代码和用户手册可在以下网址免费获取：github.com/CMU-SAFARI/FastRemap。Docker 映像可在以下网址获取：https://hub.docker.com/r/alkanlab/fastremap。也可在 Bioconda 上获取：https://anaconda.org/bioconda/fastremap-bio。
