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NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural vari...

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Detalles Bibliográficos
Autores principales: Leggett, Richard M., Clavijo, Bernardo J., Clissold, Leah, Clark, Matthew D., Caccamo, Mario
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519/
https://www.ncbi.nlm.nih.gov/pubmed/24297520
http://dx.doi.org/10.1093/bioinformatics/btt702
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author Leggett, Richard M.
Clavijo, Bernardo J.
Clissold, Leah
Clark, Matthew D.
Caccamo, Mario
author_facet Leggett, Richard M.
Clavijo, Bernardo J.
Clissold, Leah
Clark, Matthew D.
Caccamo, Mario
author_sort Leggett, Richard M.
collection PubMed
description Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols and the selection of sequenced reads for downstream analysis are non-trivial tasks. NextClip is a tool for analyzing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads. Availability and implementation: Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/. Contact: Richard.Leggett@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-39285192014-02-24 NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries Leggett, Richard M. Clavijo, Bernardo J. Clissold, Leah Clark, Matthew D. Caccamo, Mario Bioinformatics Applications Notes Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols and the selection of sequenced reads for downstream analysis are non-trivial tasks. NextClip is a tool for analyzing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads. Availability and implementation: Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/. Contact: Richard.Leggett@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-02-15 2013-12-02 /pmc/articles/PMC3928519/ /pubmed/24297520 http://dx.doi.org/10.1093/bioinformatics/btt702 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Leggett, Richard M.
Clavijo, Bernardo J.
Clissold, Leah
Clark, Matthew D.
Caccamo, Mario
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title_full NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title_fullStr NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title_full_unstemmed NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title_short NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
title_sort nextclip: an analysis and read preparation tool for nextera long mate pair libraries
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519/
https://www.ncbi.nlm.nih.gov/pubmed/24297520
http://dx.doi.org/10.1093/bioinformatics/btt702
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