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Kraken: A set of tools for quality control and analysis of high-throughput sequence data()

New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis...

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Detalles Bibliográficos
Autores principales: Davis, Matthew P.A., van Dongen, Stijn, Abreu-Goodger, Cei, Bartonicek, Nenad, Enright, Anton J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Academic Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991327/
https://www.ncbi.nlm.nih.gov/pubmed/23816787
http://dx.doi.org/10.1016/j.ymeth.2013.06.027
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author Davis, Matthew P.A.
van Dongen, Stijn
Abreu-Goodger, Cei
Bartonicek, Nenad
Enright, Anton J.
author_facet Davis, Matthew P.A.
van Dongen, Stijn
Abreu-Goodger, Cei
Bartonicek, Nenad
Enright, Anton J.
author_sort Davis, Matthew P.A.
collection PubMed
description New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis.
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spelling pubmed-39913272014-04-18 Kraken: A set of tools for quality control and analysis of high-throughput sequence data() Davis, Matthew P.A. van Dongen, Stijn Abreu-Goodger, Cei Bartonicek, Nenad Enright, Anton J. Methods Article New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis. Academic Press 2013-09-01 /pmc/articles/PMC3991327/ /pubmed/23816787 http://dx.doi.org/10.1016/j.ymeth.2013.06.027 Text en © 2013 The Authors http://creativecommons.org/licenses/by-nc-nd/3.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
spellingShingle Article
Davis, Matthew P.A.
van Dongen, Stijn
Abreu-Goodger, Cei
Bartonicek, Nenad
Enright, Anton J.
Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title_full Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title_fullStr Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title_full_unstemmed Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title_short Kraken: A set of tools for quality control and analysis of high-throughput sequence data()
title_sort kraken: a set of tools for quality control and analysis of high-throughput sequence data()
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991327/
https://www.ncbi.nlm.nih.gov/pubmed/23816787
http://dx.doi.org/10.1016/j.ymeth.2013.06.027
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