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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Quality control and preprocessing of metagenomic datasets.
Robert Schmieder1, Robert Edwards
1Department of Computer Science, Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA. rschmied@sciences.sdsu.edu
Bioinformatics (Oxford, England)
|February 1, 2011
Summary
PRINSEQ offers fast quality control and data preprocessing for genomic and metagenomic datasets. This tool generates statistics and allows filtering, reformatting, and trimming of sequence data to enhance downstream analyses.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genomic and metagenomic datasets require rigorous quality control and preprocessing.
- Existing tools may lack comprehensive features or user-friendliness for diverse sequence data formats.
Purpose of the Study:
- To introduce PRINSEQ, a versatile software for genomic and metagenomic data preprocessing.
- To provide efficient quality control and data manipulation capabilities for sequence analysis.
Main Methods:
- PRINSEQ is an open-source application developed in Perl.
- It offers both standalone and web-based interfaces for accessibility.
- The software generates summary statistics in tabular and graphical formats.
Main Results:
- PRINSEQ facilitates easy and rapid quality control of FASTA and FASTQ files.
- It enables filtering, reformatting, and trimming of sequences.
- The tool produces comprehensive summary statistics to guide data preprocessing.
Conclusions:
- PRINSEQ is a valuable tool for improving the quality of genomic and metagenomic datasets.
- Its features enhance the efficiency and accuracy of downstream bioinformatics analyses.
- The software is readily available with comprehensive documentation and support.
