title: FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.
abstract: CONCLUSIONS
  MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM.
  
  
  METHODS
  The software and the datasets are available at http://www.di.unisa.it/FASTdoop/ .
  
  
  BACKGROUND
  umberto.ferraro@uniroma1.it.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Dipartimento di Scienze Statistiche, Università di Roma-"La Sapienza", Rome, Italy.
authors.forename: Umberto
authors.initials: U
authors.lastname: Ferraro Petrillo
authors.affiliation: Dipartimento di Informatica, Università di Salerno, Fisciano (SA), Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Roscigno
authors.affiliation: Dipartimento di Informatica, Università di Salerno, Fisciano (SA), Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Cattaneo
authors.affiliation: Dipartimento di Matematica ed Informatica, Università di Palermo, Palermo, Italy.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Giancarlo
mesh_terms: D003628:Database Management Systems; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval; D017422:Sequence Analysis, DNA / Q000379:methods*