Consistent ultra-long DNA sequencing with automated slow pipetting
Abstract Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules throug...
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| Format: | Article |
| Language: | English |
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BMC
2021-03-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07500-w |
| _version_ | 1818619387565834240 |
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| author | Trent M. Prall Emma K. Neumann Julie A. Karl Cecilia G. Shortreed David A. Baker Hailey E. Bussan Roger W. Wiseman David H. O’Connor |
| author_facet | Trent M. Prall Emma K. Neumann Julie A. Karl Cecilia G. Shortreed David A. Baker Hailey E. Bussan Roger W. Wiseman David H. O’Connor |
| author_sort | Trent M. Prall |
| collection | DOAJ |
| description | Abstract Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules through library preparation by pipetting reagents as slowly as possible to minimize shearing. This process is time-consuming and inconsistent at preserving read length as even small changes in volumetric flow rate can result in template shearing. Results We have designed SNAILS (Slow Nucleic Acid Instrument for Long Sequences), a 3D-printable instrument that automates slow pipetting of reagents used in long read library preparation for Oxford Nanopore sequencing. Across six sequencing libraries, SNAILS preserved more reads exceeding 100 kilobases in length and increased its libraries’ average read length over manual slow pipetting. Conclusions SNAILS is a low-cost, easily deployable solution for improving sequencing projects that require reads of significant length. By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing. |
| first_indexed | 2024-12-16T17:36:41Z |
| format | Article |
| id | doaj.art-7abaa99c2c9742b3894e3dd25ba0d864 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-16T17:36:41Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7abaa99c2c9742b3894e3dd25ba0d8642022-12-21T22:22:43ZengBMCBMC Genomics1471-21642021-03-0122111210.1186/s12864-021-07500-wConsistent ultra-long DNA sequencing with automated slow pipettingTrent M. Prall0Emma K. Neumann1Julie A. Karl2Cecilia G. Shortreed3David A. Baker4Hailey E. Bussan5Roger W. Wiseman6David H. O’Connor7Department of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinDepartment of Pathology and Laboratory Medicine, University of WisconsinAbstract Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules through library preparation by pipetting reagents as slowly as possible to minimize shearing. This process is time-consuming and inconsistent at preserving read length as even small changes in volumetric flow rate can result in template shearing. Results We have designed SNAILS (Slow Nucleic Acid Instrument for Long Sequences), a 3D-printable instrument that automates slow pipetting of reagents used in long read library preparation for Oxford Nanopore sequencing. Across six sequencing libraries, SNAILS preserved more reads exceeding 100 kilobases in length and increased its libraries’ average read length over manual slow pipetting. Conclusions SNAILS is a low-cost, easily deployable solution for improving sequencing projects that require reads of significant length. By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing.https://doi.org/10.1186/s12864-021-07500-wOxford Nanopore technologiesGridIONMinIONDNA sequencingLong read sequencingUltra-long |
| spellingShingle | Trent M. Prall Emma K. Neumann Julie A. Karl Cecilia G. Shortreed David A. Baker Hailey E. Bussan Roger W. Wiseman David H. O’Connor Consistent ultra-long DNA sequencing with automated slow pipetting BMC Genomics Oxford Nanopore technologies GridION MinION DNA sequencing Long read sequencing Ultra-long |
| title | Consistent ultra-long DNA sequencing with automated slow pipetting |
| title_full | Consistent ultra-long DNA sequencing with automated slow pipetting |
| title_fullStr | Consistent ultra-long DNA sequencing with automated slow pipetting |
| title_full_unstemmed | Consistent ultra-long DNA sequencing with automated slow pipetting |
| title_short | Consistent ultra-long DNA sequencing with automated slow pipetting |
| title_sort | consistent ultra long dna sequencing with automated slow pipetting |
| topic | Oxford Nanopore technologies GridION MinION DNA sequencing Long read sequencing Ultra-long |
| url | https://doi.org/10.1186/s12864-021-07500-w |
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