Sigmoni: classification of nanopore signal with a compressed pangenome index

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(Supplement_1), P. i287 - i296

Published: April 11, 2024

Abstract Summary Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck basecalling. But past methods signal-based do not scale efficiently to large, repetitive references like pangenomes, limiting their utility partial or individual genomes. We introduce Sigmoni: a rapid, multiclass method based on r-index scales hundreds Gbps. Sigmoni quantizes signal into discrete alphabet picoamp ranges. It performs approximate matching using statistics, classifying distributions statistics co-linearity all linear query time without need seed-chain-extend. is 10–100× faster than previous host depletion experiments with improved accuracy, can against large microbial human pangenomes. first tool complete genome pangenome while remaining fast enough applications. Availability implementation implemented Python, available open-source at https://github.com/vshiv18/sigmoni.

Language: Английский

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Icarust, a real-time simulator for Oxford Nanopore adaptive sampling

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(4)

Published: March 13, 2024

Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this capability in extremis, rejecting or accepting reads sequencing based on assessment the from start each read. This functionality is provided by ONT's software, MinKNOW (Oxford Technologies). Designing and developing software to take advantage adaptive can be costly terms consumables, using precious samples preparing libraries. addresses part allowing replay previously sequenced runs testing. However, as we show, output only partially changes response instructions. Here present Icarust, tool enabling more accurate approximations runs. Icarust recreates all required endpoints perform writes compatible with current base-callers pipelines. serves nanopore signal simulating MinION PromethION flow cell experiment any reference genome either R9 R10 pore models. We show that provides realistic testing development environment exploiting nature sequencing.

Language: Английский

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Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(2)

Published: April 4, 2024

Abstract Summary: Nanopore sequencing technologies have enabled the direct detection of base modifications in DNA or RNA molecules. Despite these advancements, tools for visualizing electrical current, essential analyzing modifications, are often lacking clarity and compatibility with diverse nanopore pipelines. Here, we present Current Events Magnifier (nanoCEM, https://github.com/lrslab/nanoCEM), a Python command-line tool designed to facilitate identification DNA/RNA modification sites through enhanced visualization statistical analysis. Compatible four preprocessing methods including ‘f5c resquiggle’, eventalign’, ‘Tombo’ ‘move table’, nanoCEM is applicable analysis across multiple flow cell types. By utilizing rescaling techniques calculating various features, provides more accurate comparable current events, allowing researchers effectively observe differences between samples showcase modified sites.

Language: Английский

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De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 2, 2025

Language: Английский

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Interactive visualisation of nanopore sequencing signal data with Squigualiser

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(8)

Published: Aug. 1, 2024

Abstract Motivation Nanopore sequencing current signal data can be ‘basecalled’ into sequence information or analysed directly, with the capacity to identify diverse molecular features, such as DNA/RNA base modifications and secondary structures. However, raw is large complex, there a need for improved visualization strategies facilitate analysis, exploration tool development. Results Squigualiser (Squiggle visualiser) toolkit intuitive, interactive of sequence-aligned data, which currently supports both DNA RNA from Oxford Technologies instruments. compatible wide range alternative signal-alignment software packages enables signal-to-read signal-to-reference aligned at single-base resolution. generates an browser view (HTML file), in user navigate across genome/transcriptome region customize display. Multiple independent reads are integrated ‘signal pileup’ format different datasets displayed parallel tracks. Although other methods exist, provides community package purpose-built visualization, incorporating new existing features unified platform. Availability implementation open-source under MIT licence: https://github.com/hiruna72/squigualiser. The was developed using Python 3.8 installed pip bioconda executed directly prebuilt binaries provided each release.

Language: Английский

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Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Nov. 17, 2023

minimap2 is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. While relatively fast, further speedup desirable, especially when processing a multitude of large datasets. In this work, we present minimap2-fpga, hardware-accelerated version that speeds up process by integrating an FPGA kernel optimised chaining. Integrating into posed significant challenges solved accurately predicting time on hardware while considering data transfer overheads, mitigating scheduling overheads multi-threaded environment, and optimizing memory management realistic We demonstrate speed-ups end-to-end run-time from both Oxford Nanopore Technologies (ONT) Pacific Biosciences (PacBio). minimap2-fpga to 79% 53% faster than [Formula: see text] ONT PacBio datasets respectively, without base-level alignment. When with alignment, 62% 10% respectively. The accuracy near-identical original data, supported Intel FPGA-based systems (evaluations performed on-premise system) Xilinx cloud system). also provide well-documented library FPGA-accelerated chaining be used future researchers developing alignment limited background.

Language: Английский

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Streamlining remote nanopore data access with slow5curl

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background As adoption of nanopore sequencing technology continues to advance, the need maintain large volumes raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl, software package designed streamline sharing, accessibility, and reanalysis. Results Slow5curl allows user fetch specified read or group reads from dataset stored on remote server, such as public repository, without downloading entire file. uses an index quickly specific in SLOW5/BLOW5 format highly parallelized access requests maximize download speeds. Using all Human Pangenome Reference Consortium (>22 TB), demonstrate how slow5curl can be used reanalyze corresponding set target genes each individual cohort (n = 91), minimizing time, egress costs, local storage requirements their Conclusions We provide free, open-source that will reduce frictions sharing community: https://github.com/BonsonW/slow5curl.

Language: Английский

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DeepSME: De Novo Nanopore Basecalling of Motif-insensitive DNA Methylation and Alignment-free Digital Information Decryptions at Single-Molecule Level

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 17, 2024

Biomolecular encryption employing chemical modifications enables secure approaches for information storage and communications. However, constructing high density pathways rapid synthesis readout remains a challenge to guarantee confidentiality, integrity, availability (CIA). Here we develop nanopore sequencing based protocol, demonstrated by complete substitution using 5-hydroxymethylcytosine (5hmC) individual nucleotide recognition rather than sequential interactions. Such motif-insensitive methylation at the single-molecule level does not naturally exist results in severe ion current disruption 67.2%-100% failure, which ensure its ability on of data encoded inside DNA. We further propose establish an alignment-free DeepSME basecaller, is deep learning-based platform independent prior models knowledges. utilizes three-stage training pipeline that initiates tolerable 11.55% errors, expands neighboring k-mer dictionary model size from 4^6 4^9, mitigates errors only three microbial genomes, giving rise 92% precision with recall. Fully 5hmC encrypted digital were deciphered within 16× coverage depth. The versatile transparent F1-score performance 86.4% surpassing all state-of-the-art basecallers, support great potential meeting rapidly increasing CIA demands DNA-based

Language: Английский

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A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world’s tallest trees

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Sept. 30, 2024

Language: Английский

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TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 4, 2024

Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore design, which creates significantly more barcodes: 137 with length of 20 base pairs, 410 at 24 bp, and 1779 30 far surpassing ONT's offerings. It includes GPU-based acceleration ultra-fast demultiplexing designs robust barcodes suitable high-error ONT data. TDFPS-Designer outperforms current methods, improving the recall rate by 20% relative Guppy, without reduction in precision.

Language: Английский

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