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Evaluation of genome scaffolding tools using pooled clone sequencing
DNA sequencing technologies hold great promise in generating information that will guide scientists to understand how the genome effects human health and organismal evolution. The process of generating raw genome sequence data becomes cheaper and faster, but more error-prone. Assembly of such data i...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Scientific and Technological Research Council of Turkey
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451843/ https://www.ncbi.nlm.nih.gov/pubmed/30983868 http://dx.doi.org/10.3906/biy-1805-42 |
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author | DAL, Elif ALKAN, Can |
author_facet | DAL, Elif ALKAN, Can |
author_sort | DAL, Elif |
collection | PubMed |
description | DNA sequencing technologies hold great promise in generating information that will guide scientists to understand how the genome effects human health and organismal evolution. The process of generating raw genome sequence data becomes cheaper and faster, but more error-prone. Assembly of such data into high-quality finished genome sequences remains challenging. Many genome assembly tools are available, but they differ in terms of their performance and their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. Here we evaluate the accuracies of several genome scaffolding algorithms using two different types of data generated from the genome of the same human individual: whole genome shotgun sequencing (WGS) and pooled clone sequencing (PCS). We observe that it is possible to obtain better assemblies if PCS data are used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-aware scaffolding algorithms remain an open problem. |
format | Online Article Text |
id | pubmed-6451843 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | The Scientific and Technological Research Council of Turkey |
record_format | MEDLINE/PubMed |
spelling | pubmed-64518432019-04-12 Evaluation of genome scaffolding tools using pooled clone sequencing DAL, Elif ALKAN, Can Turk J Biol Article DNA sequencing technologies hold great promise in generating information that will guide scientists to understand how the genome effects human health and organismal evolution. The process of generating raw genome sequence data becomes cheaper and faster, but more error-prone. Assembly of such data into high-quality finished genome sequences remains challenging. Many genome assembly tools are available, but they differ in terms of their performance and their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. Here we evaluate the accuracies of several genome scaffolding algorithms using two different types of data generated from the genome of the same human individual: whole genome shotgun sequencing (WGS) and pooled clone sequencing (PCS). We observe that it is possible to obtain better assemblies if PCS data are used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-aware scaffolding algorithms remain an open problem. The Scientific and Technological Research Council of Turkey 2018-12-10 /pmc/articles/PMC6451843/ /pubmed/30983868 http://dx.doi.org/10.3906/biy-1805-42 Text en Copyright © 2018 The Author(s) This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Article DAL, Elif ALKAN, Can Evaluation of genome scaffolding tools using pooled clone sequencing |
title | Evaluation of genome scaffolding tools using pooled clone sequencing |
title_full | Evaluation of genome scaffolding tools using pooled clone sequencing |
title_fullStr | Evaluation of genome scaffolding tools using pooled clone sequencing |
title_full_unstemmed | Evaluation of genome scaffolding tools using pooled clone sequencing |
title_short | Evaluation of genome scaffolding tools using pooled clone sequencing |
title_sort | evaluation of genome scaffolding tools using pooled clone sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451843/ https://www.ncbi.nlm.nih.gov/pubmed/30983868 http://dx.doi.org/10.3906/biy-1805-42 |
work_keys_str_mv | AT dalelif evaluationofgenomescaffoldingtoolsusingpooledclonesequencing AT alkancan evaluationofgenomescaffoldingtoolsusingpooledclonesequencing |