FindingNemo: A Toolkit for DNA Extraction, Library Preparation and Purification for Ultra Long Nanopore Sequencing
Cahyani, I.; Tyson, J.; Holmes, N.; Quick, J.; Moore, C.; Loman, N. J.; Loose, M. W.
Show abstract
Since the advent of long read sequencing, achieving longer read lengths has been a key goal for many users. Ultra-long read sets (N50 [≥] 100 kb) produced from Oxford Nanopore sequencers have improved genome assemblies in recent years. However, despite progress in extraction protocols and library preparation methods, ultra-long sequencing remains challenging for many sample types. Here we compare various methods and introduce the FindingNemo protocol that: (1) optimises ultra-high molecular weight (UHMW) DNA extraction and library clean-up by using glass beads and Hexamminecobalt(III) chloride (CoHex), (2) can deliver high ultra-long sequencing yield of >20 Gb of reads from a single MinION flow cell or >100 Gb from PromethION devices (R9.4 to R10.4 pore variants), and (3) is scalable to using fewer input cells or lower DNA amounts, with extraction to sequencing possible in a single working day. By comparison, we show this protocol is superior to previous ones due to precise determination of input DNA quantity and quality by cell count, sample dilution and homogenization approaches.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Machine-driven parameter optimisation of biochemical reactions 95%
- Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques 95%
- ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples 95%
Similar papers in this journal
- Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing 94%
- Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls 93%
- Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.