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Using Apache Spark on genome assembly for scalable overlap-graph reduction.

ABSTRACT: BACKGROUND:De novo genome assembly is a technique that builds the genome of a specimen using overlaps of genomic fragments without additional work with reference sequence. Sequence fragments (called reads) are assembled as contigs and scaffolds by the overlaps. The quality of the de novo assembly depends on the length and continuity of the assembly. To enable faster and more accurate assembly of species, existing sequencing techniques have been proposed, for example, high-throughput next-generation sequencing and long-reads-producing third-generation sequencing. However, these techniques require a large amounts of computer memory when very huge-size overlap graphs are resolved. Also, it is challenging for parallel computation. RESULTS:To address the limitations, we propose an innovative algorithmic approach, called Scalable Overlap-graph Reduction Algorithms (SORA). SORA is an algorithm package that performs string graph reduction algorithms by Apache Spark. The SORA's implementations are designed to execute de novo genome assembly on either a single machine or a distributed computing platform. SORA efficiently compacts the number of edges on enormous graphing paths by adapting scalable features of graph processing libraries provided by Apache Spark, GraphX and GraphFrames. CONCLUSIONS:We shared the algorithms and the experimental results at our project website, https://github.com/BioHPC/SORA . We evaluated SORA with the human genome samples. First, it processed a nearly one billion edge graph on a distributed cloud cluster. Second, it processed mid-to-small size graphs on a single workstation within a short time frame. Overall, SORA achieved the linear-scaling simulations for the increased computing instances.

SUBMITTER: Paul AJ

PROVIDER: S-EPMC6805285 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements. For example, calling the somatic variants according to the GATK best practices guidelines requires days of computing time for a typical whole-genome sequencing sample.FindingsWe introduce Halvade Somatic, a framework for somatic variant calling from DNA sequencing data that takes advantage of multi-node and/or multi-core compute platforms to reduce runtime. It relies on Apache Spark to provide scalable I/O and to create and manage data streams that are processed on different CPU cores in parallel. Halvade Somatic contains all required steps to process the tumor and matched normal sample according to the GATK best practices recommendations: read alignment (BWA), sorting of reads, preprocessing steps such as marking duplicate reads and base quality score recalibration (GATK), and, finally, calling the somatic variants (Mutect2). Our approach reduces the runtime on a single 36-core node to 19.5 h compared to a runtime of 84.5 h for the original pipeline, a speedup of 4.3 times. Runtime can be further decreased by scaling to multiple nodes, e.g., we observe a runtime of 1.36 h using 16 nodes, an additional speedup of 14.4 times. Halvade Somatic supports variant calling from both whole-genome sequencing and whole-exome sequencing data and also supports Strelka2 as an alternative or complementary variant calling tool. We provide a Docker image to facilitate single-node deployment. Halvade Somatic can be executed on a variety of compute platforms, including Amazon EC2 and Google Cloud.ConclusionsTo our knowledge, Halvade Somatic is the first somatic variant calling pipeline that leverages Big Data processing platforms and provides reliable, scalable performance. Source code is freely available.

Project description:The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when dealing with increasing problems sizes, making in this way the usage of High Performance Computing (HPC) technologies such as the message passing interface (MPI) a promising alternative. Recently, MetaCacheSpark, an Apache Spark based software for detection and quantification of species composition in food samples has been proposed. This tool can be used to analyze high throughput sequencing data sets of metagenomic DNA and allows for dealing with large-scale collections of complex eukaryotic and bacterial reference genome. In this work, we propose MetaCache-MPI, a fast and memory efficient solution for computing clusters which is based on MPI instead of Apache Spark. In order to evaluate its performance a comparison is performed between the original single CPU version of MetaCache, the Spark version and the MPI version we are introducing. Results show that for 32 processes, MetaCache-MPI is 1.65× faster while consuming 48.12% of the RAM memory used by Spark for building a metagenomics database. For querying this database, also with 32 processes, the MPI version is 3.11× faster, while using 55.56% of the memory used by Spark. We conclude that the new MetaCache-MPI version is faster in both building and querying the database and uses less RAM memory, when compared with MetaCacheSpark, while keeping the accuracy of the original implementation.

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Using Apache Spark on genome assembly for scalable overlap-graph reduction.

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