Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples.

Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE 2, powered by multistep parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times more than MuSE 1 and eight to 80 times more than other popular callers. Our benchmark study suggests combining MuSE 2 and the recently accelerated Strelka2 achieves high efficiency and accuracy in analyzing large cancer genomic data sets.

Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples.

Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenge was overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE2.0, powered by multi-step parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE2.0 speeds up 50 times than MuSE1.0 and 8-80 times than other popular callers. Our benchmark study suggests combining MuSE2.0 and the recently expedited Strelka2 can achieve high efficiency and accuracy in analyzing large cancer genomic datasets.

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.

Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.