Next-generation sequence assembly: four stages of data processing and computational challenges.

Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still...

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Autores principales:	Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5320d46461c64bb188b3950e10dfa170
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id	oai:doaj.org-article:5320d46461c64bb188b3950e10dfa170
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spelling	oai:doaj.org-article:5320d46461c64bb188b3950e10dfa1702021-11-18T05:53:18ZNext-generation sequence assembly: four stages of data processing and computational challenges.1553-734X1553-735810.1371/journal.pcbi.1003345https://doaj.org/article/5320d46461c64bb188b3950e10dfa1702013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24348224/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.Sara El-MetwallyTaher HamzaMagdi ZakariaMohamed HelmyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 12, p e1003345 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Sara El-Metwally Taher Hamza Magdi Zakaria Mohamed Helmy Next-generation sequence assembly: four stages of data processing and computational challenges.
description	Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.
format	article
author	Sara El-Metwally Taher Hamza Magdi Zakaria Mohamed Helmy
author_facet	Sara El-Metwally Taher Hamza Magdi Zakaria Mohamed Helmy
author_sort	Sara El-Metwally
title	Next-generation sequence assembly: four stages of data processing and computational challenges.
title_short	Next-generation sequence assembly: four stages of data processing and computational challenges.
title_full	Next-generation sequence assembly: four stages of data processing and computational challenges.
title_fullStr	Next-generation sequence assembly: four stages of data processing and computational challenges.
title_full_unstemmed	Next-generation sequence assembly: four stages of data processing and computational challenges.
title_sort	next-generation sequence assembly: four stages of data processing and computational challenges.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/5320d46461c64bb188b3950e10dfa170
work_keys_str_mv	AT saraelmetwally nextgenerationsequenceassemblyfourstagesofdataprocessingandcomputationalchallenges AT taherhamza nextgenerationsequenceassemblyfourstagesofdataprocessingandcomputationalchallenges AT magdizakaria nextgenerationsequenceassemblyfourstagesofdataprocessingandcomputationalchallenges AT mohamedhelmy nextgenerationsequenceassemblyfourstagesofdataprocessingandcomputationalchallenges
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Next-generation sequence assembly: four stages of data processing and computational challenges.

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