title: FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.
abstract: BACKGROUND
  Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered.
  
  
  RESULTS
  FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines.
  
  
  CONCLUSIONS
  The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.
authors.forename: Jost
authors.initials: J
authors.lastname: Waldmann
authors.forename: Jan
authors.initials: J
authors.lastname: Gerken
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Hankeln
authors.forename: Timmy
authors.initials: T
authors.lastname: Schweer
authors.affiliation: Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany. fgloeckn@mpi-bremen.de.
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D015203:Reproducibility of Results; D012984:Software; D012986:Software Validation