Cloud-Native Distributed Genomic Pileup Operations

Authors

Marek Wiewiórka
Agnieszka Szmurło
Paweł Stankiewicz
Tomasz Gambin

Publication Date

1-1-2023

Journal

Bioinformatics

DOI

10.1093/bioinformatics/btac804

PMID

36515465

PMCID

PMC9848050

PubMedCentral® Posted Date

12-14-2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Software, Genomics, Algorithms, Genome, Computational Biology

Abstract

MOTIVATION: Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of all base calls from all alignments sequentially. On the other hand, a distributed version of the algorithm faces the intrinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid costly data exchange between computational nodes.

RESULTS: Here, we present a scalable, distributed and efficient implementation of a pileup algorithm that is suitable for deploying in cloud computing environments. In particular, we implemented: (i) our custom data-partitioning algorithm optimized to work with the alignment reads, (ii) a novel and unique approach to process alignment events from sequencing reads using the MD tags, (iii) the source code micro-optimizations for recurrent operations, and (iv) a modular structure of the algorithm. We have proven that our novel approach consistently and significantly outperforms other state-of-the-art distributed tools in terms of execution time (up to 6.5× faster) and memory usage (up to 2× less), resulting in a substantial cloud cost reduction. SeQuiLa is a cloud-native solution that can be easily deployed using any managed Kubernetes and Hadoop services available in public clouds, like Microsoft Azure Cloud, Google Cloud Platform, or Amazon Web Services. Together with the already implemented distributed range join and coverage calculations, our package provides end-users with a unified SQL interface for convenient analyses of population-scale genomic data in an interactive way.

AVAILABILITY AND IMPLEMENTATION: https://biodatageeks.github.io/sequila/