Halvade-RNA – a parallel, multi-node RNA-seq variant calling pipeline based on the GATK Best Practices recommendations

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice, several methods have been proposed to reduce runtime for DNA-seq analysis through the use of parallel computing.

Determining the effectively expressed variants from transcriptomics (RNA-seq) data has only recently become possible, and as such does not yet benefit from efficiently parallelized workflows. Ghent University researchers introduce Halvade-RNA, a parallel, multi-node RNA-seq variant calling pipeline based on the GATK Best Practices recommendations. Halvade-RNA makes use of the MapReduce programming model to create and manage parallel data streams on which multiple instances of existing tools such as STAR and GATK operate concurrently. Whereas the single-threaded processing of a typical RNA-seq sample requires ∼28h, Halvade-RNA reduces this runtime to ∼2h using a small cluster with two 20-core machines. Even on a single, multi-core workstation, Halvade-RNA can significantly reduce runtime compared to using multi-threading, thus providing for a more cost-effective processing of RNA-seq data. Halvade-RNA is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR.

Overview of the RNA-seq pipeline in Halvade-RNA


In the first job, reads are aligned in parallel in order to identify splice junctions and the reference genome index is rebuilt using this information. In the second job, final alignments are produced and after sorting and grouping the aligned reads by genomic region, the different Picard and GATK steps are executed in parallel.

Decap D, Reumers J, Herzeel C, Costanza P, Fostier J (2017) Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce. PLoS ONE 12(3): e0174575. [article]

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