articleBioinformaticsJan 28, 2011HYBRID OA

Quality control and preprocessing of metagenomic datasets

RSRobert SchmiederRARobert A. Edwards

Argonne National Laboratory · San Diego State University

PubMed
Indexed incrossrefdoajpubmed

Abstract

SUMMARY: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. AVAILABILITY AND IMPLEMENTATION: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/.

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Topics & keywords

Topics
Keywords
  • Perl
  • Computer science
  • Preprocessor
  • Metagenomics
  • Graphical user interface
  • Source code
  • Open source
  • Variety (cybernetics)
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