A machine-readable specification for genomics assays

Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libr...

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Detalles Bibliográficos
Autores principales: Booeshaghi, A. Sina, Chen, Xi, Pachter, Lior
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055303/
https://www.ncbi.nlm.nih.gov/pubmed/36993635
http://dx.doi.org/10.1101/2023.03.17.533215
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author Booeshaghi, A. Sina
Chen, Xi
Pachter, Lior
author_facet Booeshaghi, A. Sina
Chen, Xi
Pachter, Lior
author_sort Booeshaghi, A. Sina
collection PubMed
description Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries. We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays. The specification and associated seqspec command line tool is available at https://github.com/IGVF/seqspec.
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spelling pubmed-100553032023-03-30 A machine-readable specification for genomics assays Booeshaghi, A. Sina Chen, Xi Pachter, Lior bioRxiv Article Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries. We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays. The specification and associated seqspec command line tool is available at https://github.com/IGVF/seqspec. Cold Spring Harbor Laboratory 2023-07-18 /pmc/articles/PMC10055303/ /pubmed/36993635 http://dx.doi.org/10.1101/2023.03.17.533215 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Booeshaghi, A. Sina
Chen, Xi
Pachter, Lior
A machine-readable specification for genomics assays
title A machine-readable specification for genomics assays
title_full A machine-readable specification for genomics assays
title_fullStr A machine-readable specification for genomics assays
title_full_unstemmed A machine-readable specification for genomics assays
title_short A machine-readable specification for genomics assays
title_sort machine-readable specification for genomics assays
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055303/
https://www.ncbi.nlm.nih.gov/pubmed/36993635
http://dx.doi.org/10.1101/2023.03.17.533215
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