Quality control and preprocessing of metagenomic datasets

TLDR

PRINSEQ is introduced as a tool for rapid quality control and preprocessing of genomic and metagenomic datasets. PRINSEQ generates summary statistics for FASTA/FASTQ files, allows filtering, reformatting, and trimming, and is implemented in Perl as a stand‑alone program or web interface. Source code, documentation, and contact information are available at http://prinseq.sourceforge.net/ and via the authors' emails.

Abstract

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/. Contact: [e-mail]; [e-mail]