Fig. 1: Overview of ultra-rapid computational pipeline.
From: Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
a, After the start of sequencing on the PromethION48 device, raw signal files are periodically uploaded to cloud storage. Our cloud-based pipeline scales compute-intensive base calling and alignment across 16 instances with 4× Tesla V100 GPUs each and runs concurrently with sequencing. The instances aim for maximum resource utilization, where base calling using Guppy runs on GPU and alignment using Minimap2 (ref. 17) runs on 42 virtual CPUs in parallel. b, Once the alignment file is ready, small-variant calling performed using GPU-accelerated PEPPER–Margin–DeepVariant11 on 14 instances and SV calling using Sniffles18 on 2 instances. Each instance processes a specific set of contigs. Specific details about the Google Cloud Platform-based instance configurations are provided in Supplementary Table 21. c, These variant calls are annotated to aid in the subsequent variant filtration and prioritization. Our score-based variant filtration method takes in millions of variants reported by the variant caller to surface any deleterious variant for review using Alissa. The filtration method is designed such that it reports a tractable number of variants for manual curation.
