Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
<p>Abstract</p> <p>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 a...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-04-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/242 |
| _version_ | 1831520472805670912 |
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| author | Bishop-Lilly Kimberly A Richards Allen Ge Hong Di Bonaventura MariaPia Cook Christopher Nagarajan Niranjan DeSalle Robert Read Timothy D Pop Mihai |
| author_facet | Bishop-Lilly Kimberly A Richards Allen Ge Hong Di Bonaventura MariaPia Cook Christopher Nagarajan Niranjan DeSalle Robert Read Timothy D Pop Mihai |
| author_sort | Bishop-Lilly Kimberly A |
| collection | DOAJ |
| description | <p>Abstract</p> <p>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.</p> |
| first_indexed | 2024-12-13T17:34:14Z |
| format | Article |
| id | doaj.art-92273a0653d74dabb208fb465e1046fe |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T17:34:14Z |
| publishDate | 2010-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-92273a0653d74dabb208fb465e1046fe2022-12-21T23:36:59ZengBMCBMC Genomics1471-21642010-04-0111124210.1186/1471-2164-11-242Finishing genomes with limited resources: lessons from an ensemble of microbial genomesBishop-Lilly Kimberly ARichards AllenGe HongDi Bonaventura MariaPiaCook ChristopherNagarajan NiranjanDeSalle RobertRead Timothy DPop Mihai<p>Abstract</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/11/242 |
| spellingShingle | Bishop-Lilly Kimberly A Richards Allen Ge Hong Di Bonaventura MariaPia Cook Christopher Nagarajan Niranjan DeSalle Robert Read Timothy D Pop Mihai Finishing genomes with limited resources: lessons from an ensemble of microbial genomes BMC Genomics |
| 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 |
| url | http://www.biomedcentral.com/1471-2164/11/242 |
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