Productive visualization of high-throughput sequencing data using the SeqCode open portable platform

Abstract Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mini...

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Autores principales:	Enrique Blanco, Mar González-Ramírez, Luciano Di Croce
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/47b491730b1d4a59b4525eed5a6cb69f
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spelling	oai:doaj.org-article:47b491730b1d4a59b4525eed5a6cb69f2021-12-02T17:18:21ZProductive visualization of high-throughput sequencing data using the SeqCode open portable platform10.1038/s41598-021-98889-72045-2322https://doaj.org/article/47b491730b1d4a59b4525eed5a6cb69f2021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98889-7https://doaj.org/toc/2045-2322Abstract Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu , and the source code is freely distributed at https://github.com/eblancoga/seqcode .Enrique BlancoMar González-RamírezLuciano Di CroceNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-22 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Enrique Blanco Mar González-Ramírez Luciano Di Croce Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
description	Abstract Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu , and the source code is freely distributed at https://github.com/eblancoga/seqcode .
format	article
author	Enrique Blanco Mar González-Ramírez Luciano Di Croce
author_facet	Enrique Blanco Mar González-Ramírez Luciano Di Croce
author_sort	Enrique Blanco
title	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
title_short	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
title_full	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
title_fullStr	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
title_full_unstemmed	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
title_sort	productive visualization of high-throughput sequencing data using the seqcode open portable platform
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/47b491730b1d4a59b4525eed5a6cb69f
work_keys_str_mv	AT enriqueblanco productivevisualizationofhighthroughputsequencingdatausingtheseqcodeopenportableplatform AT margonzalezramirez productivevisualizationofhighthroughputsequencingdatausingtheseqcodeopenportableplatform AT lucianodicroce productivevisualizationofhighthroughputsequencingdatausingtheseqcodeopenportableplatform
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Productive visualization of high-throughput sequencing data using the SeqCode open portable platform

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