These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
234 related articles for article (PubMed ID: 39388235)
1. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. Hall MB; Wick RR; Judd LM; Nguyen AN; Steinig EJ; Xie O; Davies M; Seemann T; Stinear TP; Coin L Elife; 2024 Oct; 13():. PubMed ID: 39388235 [TBL] [Abstract][Full Text] [Related]
2. A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark. Pei Y; Tanguy M; Giess A; Dixit A; Wilson LC; Gibbons RJ; Twigg SRF; Elgar G; Wilkie AOM Genes (Basel); 2024 Jul; 15(7):. PubMed ID: 39062704 [TBL] [Abstract][Full Text] [Related]
3. Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction. Sanderson ND; Kapel N; Rodger G; Webster H; Lipworth S; Street TL; Peto T; Crook D; Stoesser N Microb Genom; 2023 Jan; 9(1):. PubMed ID: 36748454 [TBL] [Abstract][Full Text] [Related]
4. Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Foster-Nyarko E; Cottingham H; Wick RR; Judd LM; Lam MMC; Wyres KL; Stanton TD; Tsang KK; David S; Aanensen DM; Brisse S; Holt KE Microb Genom; 2023 Feb; 9(2):. PubMed ID: 36752781 [TBL] [Abstract][Full Text] [Related]
5. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. Bogaerts B; Van den Bossche A; Verhaegen B; Delbrassinne L; Mattheus W; Nouws S; Godfroid M; Hoffman S; Roosens NHC; De Keersmaecker SCJ; Vanneste K J Clin Microbiol; 2024 May; 62(5):e0157623. PubMed ID: 38441926 [TBL] [Abstract][Full Text] [Related]
6. Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates. Luan T; Commichaux S; Hoffmann M; Jayeola V; Jang JH; Pop M; Rand H; Luo Y BMC Genomics; 2024 Jul; 25(1):679. PubMed ID: 38978005 [TBL] [Abstract][Full Text] [Related]
7. Performance analysis of conventional and AI-based variant callers using short and long reads. Abdelwahab O; Belzile F; Torkamaneh D BMC Bioinformatics; 2023 Dec; 24(1):472. PubMed ID: 38097928 [TBL] [Abstract][Full Text] [Related]
8. Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing. Sanderson ND; Hopkins KMV; Colpus M; Parker M; Lipworth S; Crook D; Stoesser N Microb Genom; 2024 May; 10(5):. PubMed ID: 38713194 [TBL] [Abstract][Full Text] [Related]
9. Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Chen Z; Erickson DL; Meng J Genomics; 2021 May; 113(3):1366-1377. PubMed ID: 33716184 [TBL] [Abstract][Full Text] [Related]
10. Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing. Chen Z; Erickson DL; Meng J BMC Genomics; 2020 Sep; 21(1):631. PubMed ID: 32928108 [TBL] [Abstract][Full Text] [Related]
11. Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery. Barbitoff YA; Abasov R; Tvorogova VE; Glotov AS; Predeus AV BMC Genomics; 2022 Feb; 23(1):155. PubMed ID: 35193511 [TBL] [Abstract][Full Text] [Related]
12. Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing. Chen Z; Erickson DL; Meng J Int J Mol Sci; 2020 Dec; 21(23):. PubMed ID: 33271875 [TBL] [Abstract][Full Text] [Related]
13. Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology. Liu L; Zhang J; Wood S; Newell F; Leonard C; Koufariotis LT; Nones K; Dalley AJ; Chittoory H; Bashirzadeh F; Son JH; Steinfort D; Williamson JP; Bint M; Pahoff C; Nguyen PT; Twaddell S; Arnold D; Grainge C; Simpson PT; Fielding D; Waddell N; Pearson JV BMC Genomics; 2024 Sep; 25(1):898. PubMed ID: 39350042 [TBL] [Abstract][Full Text] [Related]
14. Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Helal AA; Saad BT; Saad MT; Mosaad GS; Aboshanab KM Genes (Basel); 2022 Sep; 13(9):. PubMed ID: 36140751 [TBL] [Abstract][Full Text] [Related]
15. Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis. Baeza JA; García-De León FJ BMC Genomics; 2022 Apr; 23(1):320. PubMed ID: 35459089 [TBL] [Abstract][Full Text] [Related]
16. Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks. Su J; Zheng Z; Ahmed SS; Lam TW; Luo R Brief Bioinform; 2022 Sep; 23(5):. PubMed ID: 35849103 [TBL] [Abstract][Full Text] [Related]
17. ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell. Leung AW; Leung HC; Wong CL; Zheng ZX; Lui WW; Luk HM; Lo IF; Luo R; Lam TW BMC Med Genomics; 2022 Mar; 15(1):43. PubMed ID: 35246132 [TBL] [Abstract][Full Text] [Related]
18. Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Chen Z; Grim CJ; Ramachandran P; Meng J Microbiol Spectr; 2024 Jun; 12(6):e0011724. PubMed ID: 38687063 [TBL] [Abstract][Full Text] [Related]
19. Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome. Marin M; Vargas R; Harris M; Jeffrey B; Epperson LE; Durbin D; Strong M; Salfinger M; Iqbal Z; Akhundova I; Vashakidze S; Crudu V; Rosenthal A; Farhat MR Bioinformatics; 2022 Mar; 38(7):1781-1787. PubMed ID: 35020793 [TBL] [Abstract][Full Text] [Related]
20. Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota. Heikema AP; Horst-Kreft D; Boers SA; Jansen R; Hiltemann SD; de Koning W; Kraaij R; de Ridder MAJ; van Houten CB; Bont LJ; Stubbs AP; Hays JP Genes (Basel); 2020 Sep; 11(9):. PubMed ID: 32967250 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]