Quality control and preprocessing of metagenomic datasets

• Published in: Bioinformatics Vol. 27; no. 6; pp. 863 - 864
• Main Authors: Schmieder, Robert, Edwards, Robert
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.03.2011; International Society for Computational Biology - Oxford University Press
• Subjects: Applications Note; BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biological and medical sciences; Biotechnology & Applied Microbiology; Computer Graphics; Computer Science; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Internet; Mathematical & Computational Biology; Mathematics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Metagenomics; Programming Languages; Quality Control; Sequence Analysis, DNA - methods; Software; Control; Metagenome; Quality; Quality control
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btr026

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/. Contact:  rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu