Institut Curie, Paris, F-75005, France.
U900, Inserm, Paris, F-75005, France.
F1000Res. 2020 Apr 6;9:240. doi: 10.12688/f1000research.22954.3. eCollection 2020.
Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also raise major challenges to use them for daily clinical practice care and diagnosis purposes as they are bigger and bigger. Therefore, we implemented a software to reduce the time to delivery for the alignment and the sorting of high-throughput sequencing data. Our solution is implemented using Message Passing Interface and is intended for high-performance computing architecture. The software scales linearly with respect to the size of the data and ensures a total reproducibility with the traditional tools. For example, a 300X whole genome can be aligned and sorted within less than 9 hours with 128 cores. The software offers significant speed-up using multi-cores and multi-nodes parallelization.
生命科学已经进入了所谓的“大数据时代”，生物学家、临床医生和生物信息学家都被高通量测序数据所淹没。虽然它们为破译基因组结构提供了新的见解，但由于数据越来越大，它们也给日常临床实践护理和诊断带来了重大挑战。因此，我们开发了一种软件来缩短高通量测序数据对齐和排序的交付时间。我们的解决方案使用消息传递接口实现，旨在用于高性能计算架构。该软件在数据规模上呈线性扩展，并确保与传统工具具有完全的可重复性。例如，使用 128 个核可以在不到 9 小时的时间内对齐和排序 300X 的全基因组。该软件通过多核和多节点并行化实现了显著的加速。
