Research map: Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing for Salmonella Typhi genomic surveillance

Back to the article

Papers in this map

  1. fastp: an ultra-fast all-in-one FASTQ preprocessor · Shifu Chen · 2018 · 31731 citations · Cited by this paper
  2. Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi · Danielle J. Ingle · 2025 · 6 citations · Related
  3. QUAST: quality assessment tool for genome assemblies · Alexey A. Gurevich · 2013 · 12014 citations · Cited by this paper
  4. Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing · 2026 · Related
  5. UFBoot2: Improving the Ultrafast Bootstrap Approximation · Diep Thi Hoang · 2017 · 11656 citations · Cited by this paper
  6. Evolving strategies for virus discovery · 2026 · Related
  7. MultiQC: summarize analysis results for multiple tools and samples in a single report · Philip Ewels · 2016 · 11140 citations · Cited by this paper
  8. Integrated poultry production as a reservoir of tet(X4) and mcr-1.1 encoding Escherichia coli in Pakistan · 2026 · Related
  9. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement · Bruce J. Walker · 2014 · 10515 citations · Cited by this paper
  10. Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium · 2026 · Related
  11. Assembly of long, error-prone reads using repeat graphs · Mikhail Kolmogorov · 2019 · 6698 citations · Cited by this paper
  12. Genomic analysis of intrahospital transmission of carbapenem-resistant Gram-negative bacteria: a multicentre study in Japan · 2026 · Related
  13. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool · Ivica Letunić · 2024 · 4623 citations · Cited by this paper
  14. Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen · 2026 · Related
  15. Using SPAdes De Novo Assembler · Andrey D. Prjibelski · 2020 · 3775 citations · Cited by this paper
  16. Reproducible profiling of the gut microbiota using surplus clinical faecal immunochemical test samples · 2026 · Related
  17. Performance of neural network basecalling tools for Oxford Nanopore sequencing · Ryan R. Wick · 2019 · 3342 citations · Cited by this paper
  18. Phylogenetically diverse Mucorales–Mycetohabitans endosymbiotic interactions identified from whole-genome sequencing using a targeted metagenomic assembly pipeline · 2026 · Related
  19. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins · Nicholas J. Croucher · 2014 · 3017 citations · Cited by this paper
  20. MUMmer4: A fast and versatile genome alignment system · Guillaume Marçais · 2018 · 2905 citations · Cited by this paper
  21. BIGSdb: Scalable analysis of bacterial genome variation at the population level · Keith A. Jolley · 2010 · 2497 citations · Cited by this paper
  22. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies · James A. Robertson · 2018 · 1075 citations · Cited by this paper
  23. IQ-TREE 3: phylogenomic inference software using complex evolutionary models · Thomas K. F. Wong · 2026 · 405 citations · Cited by this paper
  24. SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data · Shaokang Zhang · 2019 · 377 citations · Cited by this paper
  25. Whole genome sequencing in clinical and public health microbiology · Jason C. Kwong · 2015 · 349 citations · Cited by this paper
  26. Global disparities in SARS-CoV-2 genomic surveillance · Anderson Fernandes Brito · 2022 · 311 citations · Cited by this paper
  27. Dissemination of scientific software with Galaxy ToolShed · Daniel Blankenberg · 2014 · 288 citations · Cited by this paper
  28. Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool · Thomas Hoenen · 2015 · 241 citations · Cited by this paper
  29. Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing · Ryan R. Wick · 2023 · 202 citations · Cited by this paper
  30. Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance · James A. Robertson · 2020 · 180 citations · Cited by this paper
  31. Rasusa: Randomly subsample sequencing reads to a specified coverage · Michael B. Hall · 2022 · 168 citations · Cited by this paper
  32. Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing · Ellen Knierim · 2011 · 152 citations · Cited by this paper
  33. Selective Amplification of tyv (rfbE), prt (rfbS), viaB , and fliC Genes by Multiplex PCR for Identification of Salmonella enterica Serovars Typhi and Paratyphi A · Kenji Hirose · 2002 · 107 citations · Cited by this paper
  34. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies · George Spyro Bouras · 2024 · 105 citations · Cited by this paper
  35. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens · Bert Bogaerts · 2024 · 88 citations · Cited by this paper
  36. Advancing pathogen genomics in resource-limited settings · Paul Pronyk · 2023 · 86 citations · Cited by this paper
  37. High-throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children · Kathryn E. Holt · 2010 · 81 citations · Cited by this paper
  38. Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing · Wenxuan Zhao · 2023 · 81 citations · Cited by this paper
  39. Investigation of Outbreaks ofSalmonella entericaSerovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark · Pernille Gymoese · 2017 · 69 citations · Cited by this paper

Source: OpenAlex (CC0)