title: Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.
abstract: The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy.
authors.affiliation: Int. Research Training Group 1906 (DiDy), Bielefeld University, Bielefeld, 33501, Germany. Electronic address: yujia@cebitec.uni-bielefeld.de.
authors.forename: Jia
authors.initials: J
authors.lastname: Yu
authors.affiliation: Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, 33501, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.affiliation: Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
mesh_terms: D000067917:Cloud Computing; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D020407:Internet; D054892:Metagenome; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000295:instrumentation / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D012984:Software; D000073336:Whole Genome Sequencing
keywords: Cloud computing; Parallel computing; Sequence alignment