Polypolish: Short-read polishing of long-read bacterial genome assemblies

PLoS Computational Biology, Год журнала: 2022, Номер 18(1), С. e1009802 - e1009802

Опубликована: Янв. 24, 2022

Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these but rely on short-read alignment which is unreliable in repeat regions. Errors such regions are therefore challenging and often remain after polishing. Here we introduce Polypolish, a new polisher uses all-per-read alignments repair errors sequences that other polishers cannot. Polypolish performed well benchmarking tests using both simulated real reads, it almost never introduced during The best results were achieved by combination with polishers.

Язык: Английский

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Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Nature Methods, Год журнала: 2022, Номер 19(7), С. 823 - 826

Опубликована: Июль 1, 2022

Long-read Oxford Nanopore sequencing has democratized microbial genome and enables the recovery of highly contiguous genomes from isolates or metagenomes. However, to obtain near-finished it been necessary include short-read polishing correct insertions deletions derived homopolymer regions. Here, we show that R10.4 can be used generate metagenomes without reference polishing.

Язык: Английский

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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

PLoS Computational Biology, Год журнала: 2023, Номер 19(3), С. e1010905 - e1010905

Опубликована: Март 2, 2023

A perfect bacterial genome assembly is one where the assembled sequence an exact match for organism’s genome—each replicon complete and contains no errors. While this has been difficult to achieve in past, improvements long-read sequencing, assemblers, polishers have brought assemblies within reach. Here, we describe our recommended approach assembling a perfection using combination of Oxford Nanopore Technologies long reads Illumina short reads: Trycycler assembly, Medaka polishing, Polypolish short-read followed by other polishing tools manual curation. We also discuss potential pitfalls might encounter when challenging genomes, provide online tutorial with sample data ( github.com/rrwick/perfect-bacterial-genome-tutorial ).

Язык: Английский

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Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Cell, Год журнала: 2023, Номер 186(22), С. 4803 - 4817.e13

Опубликована: Сен. 7, 2023

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation. Imaging fluorescent protein-labeled provides high spatiotemporal resolution phenomena accompanying epibiotic growth, transposon-insertion sequencing (Tn-seq) genome-wide screen reveals contribution enigmatic Saccharibacterial genes growth hosts. Finally, leverage metagenomic data provide cutting-edge protein structure-based bioinformatic resources support strain Southlakia epibionticum its corresponding host, Actinomyces israelii, model system unlocking molecular underpinnings lifestyle.

Язык: Английский

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Rapid expansion and international spread of M1UK in the post-pandemic UK upsurge of Streptococcus pyogenes

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Май 10, 2024

Abstract The UK observed a marked increase in scarlet fever and invasive group A streptococcal infection 2022 with severe outcomes children similar trends worldwide. Here we report lineage M1 to be the dominant source of infections this upsurge. Compared ancestral global strains, strains exhibit reduced genomic diversity fewer mutations two-component regulator genes covRS . emergence is dated 2008. Following bottleneck coinciding COVID-19 pandemic, three emergent clades underwent rapid nationwide expansion, despite lack detection previous years. All isolates thus-far sequenced globally have phylogenetic origin UK, dispersal new Europe. While waning immunity may promote epidemics, genetic features point fitness advantage pathogenicity, striking ability persist through population bottlenecks.

Язык: Английский

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Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance

mBio, Год журнала: 2024, Номер 15(2)

Опубликована: Янв. 17, 2024

Hypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence unclear. Therefore, it critical importance to determine whether given resistant K. isolate hypervirulent. This report determined which combination genotypic and phenotypic markers could most accurately identify with acquired resistance. Both logistic regression machine-learning prediction model demonstrated biomarker count alone was strongest predictor. The presence all five biomarkers iucA, iroB, peg-344, rmpA, rmpA2 accurate (94%); ≥4 these sensitive (100%). Accurately identifying vital for surveillance research, availability data alert clinician consideration, which, turn, would assist optimizing patient care.

Язык: Английский

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Dnaapler: A tool to reorient circular microbial genomes

The Journal of Open Source Software, Год журнала: 2024, Номер 9(93), С. 5968 - 5968

Опубликована: Янв. 11, 2024

Microorganisms found in natural environments are fundamental components of ecosystems and play vital roles various ecological processes.Studying their genomes can provide valuable insights into the diversity, functionality, evolution microbial life, as well impacts on human health.Once genetic material is extracted from environmental samples, it undergoes sequencing using technologies like whole genome (WGS).The raw sequence data then analysed, computational methods applied to assemble fragmented sequences reconstruct complete (Wick et al.,

Язык: Английский

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Unveiling microbial diversity: harnessing long-read sequencing technology

Nature Methods, Год журнала: 2024, Номер 21(6), С. 954 - 966

Опубликована: Апрель 30, 2024

Язык: Английский

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How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

Microbial Genomics, Год журнала: 2024, Номер 10(6)

Опубликована: Июнь 4, 2024

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing usually required for perfection. However, the effect of depth on performance not well understood. Here, we introduce Pypolca (with default and careful parameters) Polypolish v0.6.0 a new parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default Polypolish-careful commonly false-positive errors at low read depth; (2) most benefit occurs by 25× (3) almost never introduces any (4) Pypolca-careful single effective polisher. Overall, recommend following strategies: alone when very (<5×), (5–25×), sufficient (>25×).

Язык: Английский

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Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

Microbial Genomics, Год журнала: 2024, Номер 10(5)

Опубликована: Май 8, 2024

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- long-reads) assembly approaches. Complete allow a deeper understanding evolution genomic variation beyond single nucleotide variants. They also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids missed or misassembled by algorithms. Here, we present Hybracter allows fast, automatic scalable recovery near-perfect first approach. can be run either as assembler only assembler. We compared to existing automated tools diverse panel samples varying levels with manually curated ground truth reference genomes. demonstrate is more accurate faster than gold standard Unicycler. show long-reads most comparable methods accurately recovering plasmids.

Язык: Английский

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