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Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library constructio...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864248/ https://www.ncbi.nlm.nih.gov/pubmed/20398345 http://dx.doi.org/10.1186/1471-2164-11-242 |
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author | Nagarajan, Niranjan Cook, Christopher Di Bonaventura, MariaPia Ge, Hong Richards, Allen Bishop-Lilly, Kimberly A DeSalle, Robert Read, Timothy D Pop, Mihai |
author_facet | Nagarajan, Niranjan Cook, Christopher Di Bonaventura, MariaPia Ge, Hong Richards, Allen Bishop-Lilly, Kimberly A DeSalle, Robert Read, Timothy D Pop, Mihai |
author_sort | Nagarajan, Niranjan |
collection | PubMed |
description | While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores. |
format | Text |
id | pubmed-2864248 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28642482010-05-05 Finishing genomes with limited resources: lessons from an ensemble of microbial genomes Nagarajan, Niranjan Cook, Christopher Di Bonaventura, MariaPia Ge, Hong Richards, Allen Bishop-Lilly, Kimberly A DeSalle, Robert Read, Timothy D Pop, Mihai BMC Genomics Correspondence While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores. BioMed Central 2010-04-16 /pmc/articles/PMC2864248/ /pubmed/20398345 http://dx.doi.org/10.1186/1471-2164-11-242 Text en Copyright ©2010 The Article is a work of the United States Government; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Correspondence Nagarajan, Niranjan Cook, Christopher Di Bonaventura, MariaPia Ge, Hong Richards, Allen Bishop-Lilly, Kimberly A DeSalle, Robert Read, Timothy D Pop, Mihai Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title | Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title_full | Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title_fullStr | Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title_full_unstemmed | Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title_short | Finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
title_sort | finishing genomes with limited resources: lessons from an ensemble of microbial genomes |
topic | Correspondence |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864248/ https://www.ncbi.nlm.nih.gov/pubmed/20398345 http://dx.doi.org/10.1186/1471-2164-11-242 |
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