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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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Nature Methods, Год журнала: 2023, Номер 20(10), С. 1483 - 1492

Опубликована: Сен. 14, 2023

Язык: Английский

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Nature, Год журнала: 2023, Номер 621(7978), С. 355 - 364

Опубликована: Авг. 23, 2023

Язык: Английский

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Randomizing the human genome by engineering recombination between repeat elements

Science, Год журнала: 2025, Номер 387(6733)

Опубликована: Янв. 30, 2025

We lack tools to edit DNA sequences at scales necessary study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing insert recombination handles into repetitive sequences, up 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. tracked these over time measure selection pressures, finding a preference for shorter variants avoided essential genes. characterized 29 clones with multiple rearrangements, an impact deletions on expression genes variant but not nearby This genome-scrambling strategy large sequence relocations, insertion regulatory elements explore dispensability organization.

Язык: Английский

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The complete and fully-phased diploid genome of a male Han Chinese

Cell Research, Год журнала: 2023, Номер 33(10), С. 745 - 761

Опубликована: Июль 14, 2023

Since the release of complete human genome, priority genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid genome from Han Chinese male individual (CN1), which assemblies both haploids achieve telomere-to-telomere (T2T) level. Comparison this with CHM13 haploid T2T revealed significant variations centromere. Outside centromere, discovered 11,413 structural variations, including numerous novel ones. We also detected thousands CN1 alleles that have accumulated high substitution rates few under positive selection East Asian population. Further, found outperforms as reference mapping variant calling for population owing to distinct variants two references. SNP large cohort 8869 genomes using respectively showed bias profoundly impacts rare calling, nearly 2 million SNPs miss-called different genomes. Finally, applying reference, 5.80 Mb 4.21 putative introgression sequences Neanderthal Denisovan, respectively, many specific ones undetected reference. Our analyses reveal advances studies paleo-genomic studies. This will serve an alternative future on

Язык: Английский

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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(6), С. 873 - 888

Опубликована: Май 15, 2023

The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered invasive species detection, population genetics. Here we show that deep-sequencing-based approaches capture genomic information from humans (Homo sapiens) just as readily the intended target species. We term this phenomenon genetic bycatch (HGB). Additionally, high-quality could be intentionally recovered substrates (water, sand air), holding promise beneficial medical, forensic applications. However, also raises ethical dilemmas, consent, privacy surveillance to data ownership, requiring further consideration potentially novel regulation. present evidence detectable 'wildlife' samples bycatch, demonstrate identifiable can human-focused sampling discuss translational implications such findings.

Язык: Английский

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Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia

Diagnostics, Год журнала: 2023, Номер 13(3), С. 373 - 373

Опубликована: Янв. 19, 2023

Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis thalassemia by conventional PCR-based DNA analysis time- and resource-consuming owing to phenotype variability, disease complexity, molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up an extensive thalassemia-causing possible modifiers. Data coming from advanced techniques such as targeted sequencing next-generation (NGS) third-generation (TGS) are appropriate valuable for thalassemia. While NGS superior at variant calling TGS thanks its lower error rates, longer reads nature permits haplotype-phasing that discovery on homologous genes CNV calling. The emergence many cutting-edge machine learning-based bioinformatics tools has improved accuracy Constant improvement these will enable precise detections, especially HBA HBG genes. In conclusion, laboratory transiting or following guidelines towards single assay contribute better diagnostics approach

Язык: Английский

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Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv

Nucleic Acids Research, Год журнала: 2023, Номер 51(14), С. e74 - e74

Опубликована: Июнь 20, 2023

We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, Single breakend module. Using tumor/control paired from three cancer their lymphoblastoid lines, we demonstrate that module can identify SVs be captured by short-read technologies higher precision recall than existing methods. In addition, have developed workflow to classify mobile element insertions while elucidating in-depth properties, such as 5' truncations, internal inversions, well source sites 3' transductions. Furthermore, enables the complex only identified long-reads, involving highly-repetitive centromeric sequences, LINE1- virus-mediated rearrangements. summary, approaches applied reveal various features will lead better understanding mutational processes functional consequences SVs.

Язык: Английский

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BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis

NAR Genomics and Bioinformatics, Год журнала: 2023, Номер 5(1)

Опубликована: Янв. 10, 2023

Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup their values. However, these can be used only for finding exact-matching as conventional hashing methods assign distinct different including highly similar seeds. Finding causes either (i) increasing use costly sequence alignment or (ii) limited sensitivity. We introduce

Язык: Английский

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A survey of algorithms for the detection of genomic structural variants from long-read sequencing data

Nature Methods, Год журнала: 2023, Номер 20(8), С. 1143 - 1158

Опубликована: Июнь 29, 2023

Язык: Английский

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