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

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009802-e1009802

2022

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Performance of neural network basecalling tools for Oxford Nanopore sequencing

Genome Biology, 2019-06, Vol.20 (1), p.129-129, Article 129

2019

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

PLoS computational biology, 2017-06, Vol.13 (6), p.e1005595-e1005595

2017

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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Nature communications, 2021-07, Vol.12 (1), p.4188-4188, Article 4188

2021

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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

PLoS computational biology, 2023-03, Vol.19 (3), p.e1010905-e1010905

2023

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Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006583

2018

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Trycycler: consensus long-read assemblies for bacterial genomes

Genome Biology, 2021-09, Vol.22 (1), p.266-266, Article 266

2021

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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved]

F1000 research, 2019, Vol.8, p.2138

2019

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Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

PLoS genetics, 2019-04, Vol.15 (4), p.e1008114-e1008114

2019

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Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Nature communications, 2018-07, Vol.9 (1), p.2703-10, Article 2703

2018

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Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Genome medicine, 2018-10, Vol.10 (1), p.77-77, Article 77

2018

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Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

Nature communications, 2022-05, Vol.13 (1), p.3017-3017, Article 3017

2022

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GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

BMC genomics, 2020-09, Vol.21 (1), p.658-658, Article 658

2020

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Bandage: interactive visualization of de novo genome assemblies

Bioinformatics, 2015-10, Vol.31 (20), p.3350-3352

2015

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ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting

Genome medicine, 2022-08, Vol.14 (1), p.1-97, Article 97

2022

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Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

Journal of clinical microbiology, 2018-06, Vol.56 (6)

2018

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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 4; peer review: 4 approved]

F1000 research, 2021-02, Vol.8, p.2138-2138

2021

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Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients

BMC infectious diseases, 2021-07, Vol.21 (1), p.1-683, Article 683

2021

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The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

PeerJ (San Francisco, CA), 2020-01, Vol.8, p.e8273-e8273, Article e8273

2020

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Completing bacterial genome assemblies with multiplex MinION sequencing

Microbial genomics, 2017-10, Vol.3 (10), p.e000132-e000132

2017

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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Clinical infectious diseases, 2017-07, Vol.65 (2), p.208-215

2017

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Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Journal of antimicrobial chemotherapy, 2019-03, Vol.74 (3), p.577-581

2019

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Identification of Klebsiella capsule synthesis loci from whole genome data

Microbial genomics, 2016-12, Vol.2 (12), p.e000102-e000102

2016

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Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15

Journal of antimicrobial chemotherapy, 2019-05, Vol.74 (5), p.1218-1222

2019

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Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2

Molecular biology and evolution, 2023-03, Vol.40 (3)

2023

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

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Trycycler: consensus long-read assemblies for bacterial genomes

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved]

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

Bandage: interactive visualization of de novo genome assemblies

ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 4; peer review: 4 approved]

Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

Completing bacterial genome assemblies with multiplex MinION sequencing

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Identification of Klebsiella capsule synthesis loci from whole genome data

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15

Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2

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