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Bioinformatics. 2011 Mar 15;27(6):863-4. doi: 10.1093/bioinformatics/btr026. Epub 2011 Jan 28.

Quality control and preprocessing of metagenomic datasets.

Author information

1
Department of Computer Science, Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA. rschmied@sciences.sdsu.edu

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/.

PMID:
21278185
PMCID:
PMC3051327
DOI:
10.1093/bioinformatics/btr026
[Indexed for MEDLINE]
Free PMC Article

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