title: Halvade: scalable sequence analysis with MapReduce.
abstract: BACKGROUND
  Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine.
  
  
  RESULTS
  We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner. As an example, a DNA sequencing analysis pipeline for variant calling has been implemented according to the GATK Best Practices recommendations, supporting both whole genome and whole exome sequencing. Using a 15-node computer cluster with 360 CPU cores in total, Halvade processes the NA12878 dataset (human, 100 bp paired-end reads, 50× coverage) in <3 h with very high parallel efficiency. Even on a single, multi-core machine, Halvade attains a significant speedup compared with running the individual tools with multithreading.
authors.affiliation: Department of Information Technology, Ghent University - iMinds, Gaston Crommenlaan 8 bus 201, 9050 Ghent, Belgium, ExaScience Life Lab, Kapeldreef 75, 3001 Leuven, Belgium.
authors.forename: Dries
authors.initials: D
authors.lastname: Decap
authors.affiliation: ExaScience Life Lab, Kapeldreef 75, 3001 Leuven, Belgium, Janssen Research & Development, a division of Janssen Pharmaceutica N.V., 2340 Beerse, Belgium.
authors.forename: Joke
authors.initials: J
authors.lastname: Reumers
authors.affiliation: ExaScience Life Lab, Kapeldreef 75, 3001 Leuven, Belgium, Imec, Kapeldreef 75, 3001 Leuven, Belgium, and.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Herzeel
authors.affiliation: ExaScience Life Lab, Kapeldreef 75, 3001 Leuven, Belgium, Intel Corporation Belgium.
authors.forename: Pascal
authors.initials: P
authors.lastname: Costanza
authors.affiliation: Department of Information Technology, Ghent University - iMinds, Gaston Crommenlaan 8 bus 201, 9050 Ghent, Belgium, ExaScience Life Lab, Kapeldreef 75, 3001 Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Fostier
mesh_terms: D015894:Genome, Human; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
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