title: An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.
abstract: BACKGROUND
  Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce.
  
  
  METHODS
  An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.
  
  
  CONCLUSIONS
  Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.
authors.affiliation: Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. ronald.taylor@pnl.gov
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Taylor
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D012984:Software