Dataset Information

Evaluation of serverless computing for scalable execution of a joint variant calling workflow.

ABSTRACT: Advances in whole-genome sequencing have greatly reduced the cost and time of obtaining raw genetic information, but the computational requirements of analysis remain a challenge. Serverless computing has emerged as an alternative to using dedicated compute resources, but its utility has not been widely evaluated for standardized genomic workflows. In this study, we define and execute a best-practice joint variant calling workflow using the SWEEP workflow management system. We present an analysis of performance and scalability, and discuss the utility of the serverless paradigm for executing workflows in the field of genomics research. The GATK best-practice short germline joint variant calling pipeline was implemented as a SWEEP workflow comprising 18 tasks. The workflow was executed on Illumina paired-end read samples from the European and African super populations of the 1000 Genomes project phase III. Cost and runtime increased linearly with increasing sample size, although runtime was driven primarily by a single task for larger problem sizes. Execution took a minimum of around 3 hours for 2 samples, up to nearly 13 hours for 62 samples, with costs ranging from $2 to $70.

SUBMITTER: John A

PROVIDER: S-EPMC8270184 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Evaluation of serverless computing for scalable execution of a joint variant calling workflow.

John Aji A Muenzen Kathleen K Ausmees Kristiina K

PloS one 20210709 7

Advances in whole-genome sequencing have greatly reduced the cost and time of obtaining raw genetic information, but the computational requirements of analysis remain a challenge. Serverless computing has emerged as an alternative to using dedicated compute resources, but its utility has not been widely evaluated for standardized genomic workflows. In this study, we define and execute a best-practice joint variant calling workflow using the SWEEP workflow management system. We present an analysi ...[more]

PMID: 34242357

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Project description:Recently many new deep learning-based variant-calling methods like DeepVariant have emerged as more accurate compared with conventional variant-calling algorithms such as GATK HaplotypeCaller, Sterlka2, and Freebayes albeit at higher computational costs. Therefore, there is a need for more scalable and higher performance workflows of these deep learning methods. Almost all existing cluster-scaled variant-calling workflows that use Apache Spark/Hadoop as big data frameworks loosely integrate existing single-node pre-processing and variant-calling applications. Using Apache Spark just for distributing/scheduling data among loosely coupled applications or using I/O-based storage for storing the output of intermediate applications does not exploit the full benefit of Apache Spark in-memory processing. To achieve this, we propose a native Spark-based workflow that uses Python and Apache Arrow to enable efficient transfer of data between different workflow stages. This benefits from the ease of programmability of Python and the high efficiency of Arrow's columnar in-memory data transformations. Here we present a scalable, parallel, and efficient implementation of next-generation sequencing data pre-processing and variant-calling workflows. Our design tightly integrates most pre-processing workflow stages, using Spark built-in functions to sort reads by coordinates and mark duplicates efficiently. Our approach outperforms state-of-the-art implementations by >2 times for the pre-processing stages, creating a scalable and high-performance solution for DeepVariant for both CPU-only and CPU + GPU clusters. We show the feasibility and easy scalability of our approach to achieve high performance and efficient resource utilization for variant-calling analysis on high-performance computing clusters using the standardized Apache Arrow data representations. All codes, scripts, and configurations used to run our implementations are publicly available and open sourced; see https://github.com/abs-tudelft/variant-calling-at-scale.

Project description:Highlights • Event-driven serverless architecture requiring low cost and maintenance effort.• Data processing, storage, visualization and sharing on fault-tolerant cloud services.• Backup grid monitoring and control given access to secure Internet connection.• Cloud-hosted operation logging simplies auditing and responsibility tracking.• Cyber security mechanism that complies with CIP requirements for the power grid. Operating a modern power grid reliably in case of SCADA/EMS failure or amid difficult times like COVID-19 pandemic is a challenging task for grid operators. In [11], a PMU-based emergency generation dispatch scheme has been proposed to help the system operators with the supply and demand balancing; however, its realization highly relies on the control center infrastructure for computing and communication. This work, rather than using the on-premises server and dispatch communication system, proposes and implements a cloud-centric serverless architecture to ensure the operation continuity regardless of local infrastructure’s availability and accessibility. Through its prototype implementation and evaluation at ISO New England, the solution has demonstrated two major advantages. Firstly, the cloud infrastructure is independent and fault-tolerant, providing grid monitoring and control capability even when EMS loses the corresponding functionality or when operators need to work remotely away from the control center. Secondly, the overall design is event-driven using serverless cloud services in response to the SCADA/EMS failure event. Thanks to “serverless”, the burden of the server provisioning and maintenance can be avoided from the user side. The cost of using public cloud services for this solution is extremely low since it is architected and implemented based on the event-driven Function-as-a-Service (FaaS) model. This work also develops a comprehensive cyber security mechanism to comply with critical infrastructure requirements for the power grid, which can serve as an exemplary framework for other grid operators to secure their cloud services.

Project description:BackgroundThe advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology. The computational task of detecting and annotating sequence differences of a target dataset between a reference genome is known as "variant calling". Typically, this task is computationally involved, often combining a complex chain of linked software tools. A major player in this field is the Genome Analysis Toolkit (GATK). The "GATK Best Practices" is a commonly referred recipe for variant calling. However, current computational recommendations on variant calling predominantly focus on human sequencing data and ignore ever-changing demands of high-throughput sequencing developments. Furthermore, frequent updates to such recommendations are counterintuitive to the goal of offering a standard workflow and hamper reproducibility over time.ResultsA workflow for automated detection of single nucleotide polymorphisms and insertion-deletions offers a wide range of applications in sequence annotation of model and non-model organisms. The introduced workflow builds on the GATK Best Practices, while enabling reproducibility over time and offering an open, generalized computational architecture. The workflow achieves parallelized data evaluation and maximizes performance of individual computational tasks. Optimized Java garbage collection and heap size settings for the GATK applications SortSam, MarkDuplicates, HaplotypeCaller, and GatherVcfs effectively cut the overall analysis time in half.ConclusionsThe demand for variant calling, efficient computational processing, and standardized workflows is growing. The Open source Variant calling workFlow (OVarFlow) offers automation and reproducibility for a computationally optimized variant calling task. By reducing usage of computational resources, the workflow removes prior existing entry barriers to the variant calling field and enables standardized variant calling.

Dataset Information

Evaluation of serverless computing for scalable execution of a joint variant calling workflow.

Publications

Evaluation of serverless computing for scalable execution of a joint variant calling workflow.

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