Cargando…
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
BACKGROUND: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520994/ https://www.ncbi.nlm.nih.gov/pubmed/23251337 http://dx.doi.org/10.1371/journal.pone.0048837 |
_version_ | 1782252878458519552 |
---|---|
author | Mavromatis, Konstantinos Land, Miriam L. Brettin, Thomas S. Quest, Daniel J. Copeland, Alex Clum, Alicia Goodwin, Lynne Woyke, Tanja Lapidus, Alla Klenk, Hans Peter Cottingham, Robert W. Kyrpides, Nikos C. |
author_facet | Mavromatis, Konstantinos Land, Miriam L. Brettin, Thomas S. Quest, Daniel J. Copeland, Alex Clum, Alicia Goodwin, Lynne Woyke, Tanja Lapidus, Alla Klenk, Hans Peter Cottingham, Robert W. Kyrpides, Nikos C. |
author_sort | Mavromatis, Konstantinos |
collection | PubMed |
description | BACKGROUND: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. CONCLUSION: These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio). |
format | Online Article Text |
id | pubmed-3520994 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35209942012-12-18 The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos Land, Miriam L. Brettin, Thomas S. Quest, Daniel J. Copeland, Alex Clum, Alicia Goodwin, Lynne Woyke, Tanja Lapidus, Alla Klenk, Hans Peter Cottingham, Robert W. Kyrpides, Nikos C. PLoS One Research Article BACKGROUND: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. CONCLUSION: These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio). Public Library of Science 2012-12-12 /pmc/articles/PMC3520994/ /pubmed/23251337 http://dx.doi.org/10.1371/journal.pone.0048837 Text en © 2012 Mavromatis et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Mavromatis, Konstantinos Land, Miriam L. Brettin, Thomas S. Quest, Daniel J. Copeland, Alex Clum, Alicia Goodwin, Lynne Woyke, Tanja Lapidus, Alla Klenk, Hans Peter Cottingham, Robert W. Kyrpides, Nikos C. The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title | The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title_full | The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title_fullStr | The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title_full_unstemmed | The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title_short | The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation |
title_sort | fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520994/ https://www.ncbi.nlm.nih.gov/pubmed/23251337 http://dx.doi.org/10.1371/journal.pone.0048837 |
work_keys_str_mv | AT mavromatiskonstantinos thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT landmiriaml thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT brettinthomass thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT questdanielj thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT copelandalex thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT clumalicia thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT goodwinlynne thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT woyketanja thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT lapidusalla thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT klenkhanspeter thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT cottinghamrobertw thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT kyrpidesnikosc thefastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT mavromatiskonstantinos fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT landmiriaml fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT brettinthomass fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT questdanielj fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT copelandalex fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT clumalicia fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT goodwinlynne fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT woyketanja fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT lapidusalla fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT klenkhanspeter fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT cottinghamrobertw fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation AT kyrpidesnikosc fastchanginglandscapeofsequencingtechnologiesandtheirimpactonmicrobialgenomeassembliesandannotation |