Quality control and preprocessing of metagenomic datasets

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 op...

Descripción completa

Detalles Bibliográficos
Autores principales: Schmieder, Robert, Edwards, Robert
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051327/
https://www.ncbi.nlm.nih.gov/pubmed/21278185
http://dx.doi.org/10.1093/bioinformatics/btr026
_version_ 1782199471584575488
author Schmieder, Robert
Edwards, Robert
author_facet Schmieder, Robert
Edwards, Robert
author_sort Schmieder, Robert
collection PubMed
description 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: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu
format Text
id pubmed-3051327
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-30513272011-03-10 Quality control and preprocessing of metagenomic datasets Schmieder, Robert Edwards, Robert Bioinformatics Applications Note 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: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu Oxford University Press 2011-03-15 2011-01-28 /pmc/articles/PMC3051327/ /pubmed/21278185 http://dx.doi.org/10.1093/bioinformatics/btr026 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Schmieder, Robert
Edwards, Robert
Quality control and preprocessing of metagenomic datasets
title Quality control and preprocessing of metagenomic datasets
title_full Quality control and preprocessing of metagenomic datasets
title_fullStr Quality control and preprocessing of metagenomic datasets
title_full_unstemmed Quality control and preprocessing of metagenomic datasets
title_short Quality control and preprocessing of metagenomic datasets
title_sort quality control and preprocessing of metagenomic datasets
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051327/
https://www.ncbi.nlm.nih.gov/pubmed/21278185
http://dx.doi.org/10.1093/bioinformatics/btr026
work_keys_str_mv AT schmiederrobert qualitycontrolandpreprocessingofmetagenomicdatasets
AT edwardsrobert qualitycontrolandpreprocessingofmetagenomicdatasets

Ejemplares similares