Consistent ultra-long DNA sequencing with automated slow pipetting

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 prepa...

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Bibliographic Details
Published in:BMC genomics 2021-03, Vol.22 (1), p.182-12, Article 182
Main Authors: Prall, Trent M, Neumann, Emma K, Karl, Julie A, Shortreed, Cecilia G, Baker, David A, Bussan, Hailey E, Wiseman, Roger W, O'Connor, David H
Format: Article
Language:English
Subjects:
Automation
Chromosomes
Deoxyribonucleic acid
DNA
DNA sequencing
Equipment and supplies
Flow rates
Flow velocity
Genomes
Genomics
GridION
High-Throughput Nucleotide Sequencing
Innovations
Libraries
Long read sequencing
Methodology
Methods
MinION
Molecular weight
Mutation
Nanopore Sequencing
Nanopores
Nucleic acids
Nucleotide sequence
Nucleotide sequencing
Oxford Nanopore technologies
Porosity
Protocol
Reagents
Repetitive Sequences, Nucleic Acid
Retention
Sequence Analysis, DNA
Shearing
Snails
Three dimensional printing
Ultra-long
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Summary: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. 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. 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.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-021-07500-w