The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Completing bacterial genome assemblies with multiplex MinION sequencing
Open accessAbstract
Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure. This has major implications for tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a bacterial genome requires long-read sequencing such as those generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use of the ONT MinION to sequence 12 isolates of Klebsiella pneumoniae on a single flow cell. We assembled each genome using a combination of ONT reads and previously available Illumina reads, and little to no manual intervention was needed to achieve fully resolved assemblies using the Unicycler hybrid assembler. Assembling only ONT reads with Canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with Nanopolish. We demonstrate that multiplexed ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Specifically, we advocate the use of Illumina sequencing as a first analysis step, followed by ONT reads as needed to resolve genomic structure.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Cited by
NanoPack: visualizing and processing long-read sequencing data
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168
Performance of neural network basecalling tools for Oxford Nanopore sequencing
Wick, R. R., Judd, L. M., & Holt, K. E. (2019) · Genome Biology · doi:10.1186/s13059-019-1727-y · Cited by 3,221
Self-citationvan der Ven (2019) · doi:10.12688/f1000research · Cited by 599
Diet leaves a genetic signature in a keystone member of the gut microbiota
Dapa, T., Ramiro, R. S., Pedro, M. F., Gordo, I., & Xavier, K. B. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.01.002 · Cited by 91
Schmid, M., Frei, D., Patrignani, A., Schlapbach, R., Frey, J. E., Remus-Emsermann, M. N. P., & Ahrens, C. H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky726 · Cited by 92
Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms
Hesketh-Best, P. J., Bosco-Santos, A., Garcia, S. L., O’Beirne, M. D., Werne, J. P., Gilhooly, W. P., & Silveira, C. B. (2023) · Communications Earth & Environment · doi:10.1038/s43247-023-00796-4 · Cited by 16
Hussein, M., Sun, Z., Hawkey, J., Allobawi, R., Judd, L. M., Carbone, V., Sharma, R., Thombare, V., Baker, M., Rao, G. G., et al. (2024) · mSystems · doi:10.1128/msystems.00972-23 · Cited by 14
Self-citationSchoelmerich, M. C., Ly, L., West-Roberts, J., Shi, L.-D., Shen, C., Malvankar, N. S., Taib, N., Gribaldo, S., Woodcroft, B. J., Schadt, C. W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49548-8 · Cited by 14
Lieberman, N. A. P., Armstrong, T. D., Chung, B., Pfalmer, D., Hennelly, C. M., Haynes, A., Romeis, E., Wang, Q.-Q., Zhang, R.-L., Kou, C.-X., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1007056 · Cited by 10
Klirs, Y., Novosolov, M., Gissi, C., Garić, R., Pupko, T., Stach, T., & Huchon, D. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae181 · Cited by 7
Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis
Lee, Y., Biasini, A., Tipping, C., Hong, S. H., & Zamore, P. D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116329 · Cited by 6
Metadata
- Authors
- Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E.
- Venue
- Microbial Genomics
- Publisher
- Microbiology Society
- Published
- 2017-10-01
- Volume
- 3
- Issue
- 10
- Pages
- e000132-e000132
- ISSN
- 2057-5858 (ISSN-L)
- OpenAlex
- W2950891420
- Cited by
- 978
- References
- 4
- FWCI
- 16.60
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
