Comparison of direct RNA sequencing of Orthoavulavirus javaense using two different chemistries on the MinION platform DOI Creative Commons
Megan C. Mears, Quentin D. Read, Abhijeet Bakre

et al.

Journal of Virological Methods, Journal Year: 2024, Volume and Issue: unknown, P. 115103 - 115103

Published: Dec. 1, 2024

Rapidly identifying and sequencing viral pathogens in poultry flocks can substantially reduce economic loss especially during disease outbreaks. Current next generation technologies require multi-step laboratory-intensive workflows to generate sequence data which precludes field adaptation. In this study, we hypothesized that direct RNA (DRS) using an Oxford Nanopore Technology (ONT) MinION device would enable of the full-length genome Orthoavulavirus javaense (OAVJ), causative Newcastle disease, a major challenge. The demonstrate custom OAVJ-specific adapter paired with ONT DRS kits enables capture OAVJ RNAs. Further, new SQK-RNA004 chemistry flow cells, associated super accurate base calling workflow improves on read quality length compared previous SQK-RNA002 chemistry. This is first report method near member Paramyxoviridae family. While additional improvements are needed before widespread adaptation for rapid sequencing, has potential further studies into epitranscriptome its role infection pathogenesis.

Language: Английский

Nanopore adaptive sampling effectively enriches bacterial plasmids DOI Creative Commons
Jens-Uwe Ulrich, Lennard Epping,

Tanja Pilz

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 20, 2024

ABSTRACT Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from low abundance plasmid those samples. Although sample preparation methods can enrich proportion before sequencing, these are expensive and laborious, they might introduce bias by enriching only for specific sequences. Nanopore adaptive sampling could overcome issues rejecting uninteresting molecules during process. In this study, we assess application enrichment low-abundant known bacterial isolates using two different tools. We show that significant be achieved even on expired flow cells. By applying sampling, also improve quality de novo assemblies reduce time. our experiments highlight with if target non-target sequences span similar regions. IMPORTANCE Antimicrobial causes millions deaths every year. Mobile genetic elements like key drivers dissemination antimicrobial This makes an important tool clinical microbiologists. Since often underrepresented samples, challenging laborious. To accelerate process, evaluate nanopore as silico method plasmids. Our results potential cost-efficient future research but indicate arise reference

Language: Английский

Citations

8
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator DOI Creative Commons
Fatih Karaoğlanoğlu, Baraa Orabi, Ryan Flannigan

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(2)

Published: Jan. 25, 2024

Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle transcriptomic tasks (e.g. isoform and gene fusion detection). However, the lack of abundant gold-standard datasets hinders benchmarking such tools. Therefore, simulation LR important practical alternative. While existing simulators aim imitate machine noise target specific library protocols, they some preparation steps PCR) are difficult modify new changing techniques single-cell LRs).

Language: Английский

Citations

2
TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering DOI Creative Commons
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 28, 2024

Basecalling is an essential step in nanopore sequencing analysis where the raw signals of sequencers are converted into nucleotide sequences, that is, reads. State-of-the-art basecallers use complex deep learning models to achieve high basecalling accuracy. This makes computationally inefficient and memory-hungry, bottlenecking entire genome pipeline. However, for many applications, most reads do not match reference interest (i.e., target reference) thus discarded later steps genomics pipeline, wasting computation. To overcome this issue, we propose TargetCall, first pre-basecalling filter eliminate wasted computation basecalling. TargetCall’s key idea discard will off-target reads) prior TargetCall consists two main components: (1) LightCall, a lightweight neural network basecaller produces noisy reads, (2) Similarity Check, which labels each these as on-target or by matching them reference. Our thorough experimental evaluations show 1) improves end-to-end runtime performance state-of-the-art 3.31× while maintaining id="m2">(98.88%) recall keeping 2) maintains accuracy downstream analysis, 3) achieves better performance, throughput, recall, precision, generality than works. available at https://github.com/CMU-SAFARI/TargetCall .

Language: Английский

Citations

2
SimReadUntil for benchmarking selective sequencing algorithms on ONT devices DOI Creative Commons
Maximilian Mordig, Gunnar Rätsch, André Kahles

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(5)

Published: April 11, 2024

Abstract Motivation The Oxford Nanopore Technologies (ONT) ReadUntil API enables selective sequencing, which aims to selectively favor interesting over uninteresting reads, e.g. deplete or enrich certain genomic regions. performance gain depends on the sequencing decision-making algorithm (SSDA) decides whether reject a read, stop receiving wait for more data. Since real runs are time-consuming and costly, simulating ONT sequencer with support is highly beneficial comparing optimizing new SSDAs. Existing software like MinKNOW UNCALLED only return raw signal data, memory-intensive, require huge often unavailable multi-fast5 files (≥100GB) not clearly documented. Results We present device simulator SimReadUntil that takes set of full reads as input, distributes them channels plays back in time including mux scans, channel gaps blockages, allows well data from them. Our modified provides basecalled rather than signal, reducing computational load focusing SSDA basecalling. Tuning parameters tools ReadFish ReadBouncer becomes easier because GPU basecalling no longer required. offer various methods extract simulation summary file adapt replicate one their enrichment experiments. SimReadUntil’s gRPC interface standardized interaction wide range programming languages. Availability implementation Code fully worked examples available GitHub (https://github.com/ratschlab/sim_read_until).

Language: Английский

Citations

1
Comparison of direct RNA sequencing of Orthoavulavirus javaense using two different chemistries on the MinION platform DOI Creative Commons
Megan C. Mears, Quentin D. Read, Abhijeet Bakre

et al.

Journal of Virological Methods, Journal Year: 2024, Volume and Issue: unknown, P. 115103 - 115103

Published: Dec. 1, 2024

Rapidly identifying and sequencing viral pathogens in poultry flocks can substantially reduce economic loss especially during disease outbreaks. Current next generation technologies require multi-step laboratory-intensive workflows to generate sequence data which precludes field adaptation. In this study, we hypothesized that direct RNA (DRS) using an Oxford Nanopore Technology (ONT) MinION device would enable of the full-length genome Orthoavulavirus javaense (OAVJ), causative Newcastle disease, a major challenge. The demonstrate custom OAVJ-specific adapter paired with ONT DRS kits enables capture OAVJ RNAs. Further, new SQK-RNA004 chemistry flow cells, associated super accurate base calling workflow improves on read quality length compared previous SQK-RNA002 chemistry. This is first report method near member Paramyxoviridae family. While additional improvements are needed before widespread adaptation for rapid sequencing, has potential further studies into epitranscriptome its role infection pathogenesis.

Language: Английский

Citations

0