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One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.
Koren S, Phillippy AM. Koren S, et al. Curr Opin Microbiol. 2015 Feb;23:110-20. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1. Curr Opin Microbiol. 2015. PMID: 25461581 Free article. Review.
Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. ...In contrast, emerging long-read …
Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencin …
Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.
Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. Suzuki Y, et al. Microbiome. 2019 Aug 27;7(1):119. doi: 10.1186/s40168-019-0737-z. Microbiome. 2019. PMID: 31455406 Free PMC article.
RESULTS: Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), …
RESULTS: Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-rea …
Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples.
Baker JL. Baker JL. mSystems. 2022 Oct 26;7(5):e0049122. doi: 10.1128/msystems.00491-22. Epub 2022 Aug 22. mSystems. 2022. PMID: 35993719 Free PMC article.
Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacteri …
Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore s …
Benchmarking of long-read assemblers for prokaryote whole genome sequencing.
Wick RR, Holt KE. Wick RR, et al. F1000Res. 2019 Dec 23;8:2138. doi: 10.12688/f1000research.21782.4. eCollection 2019. F1000Res. 2019. PMID: 31984131 Free PMC article.
Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled - one contig per chromosome or plasmid. However, t …
Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow …
Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction.
Todd SM, Settlage RE, Lahmers KK, Slade DJ. Todd SM, et al. mSphere. 2018 Jul 5;3(4):e00269-18. doi: 10.1128/mSphere.00269-18. mSphere. 2018. PMID: 29976645 Free PMC article.
Compared to currently available draft assemblies (previously 24 to 67 contigs), these genomes are highly accurate and consist of only one complete chromosome. ...These genomes are highly accurate, and seven of the genomes re …
Compared to currently available draft assemblies (previously 24 to 67 contigs), these genomes are highly accurate and c …
Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.
Salazar AN, Gorter de Vries AR, van den Broek M, Wijsman M, de la Torre Cortés P, Brickwedde A, Brouwers N, Daran JG, Abeel T. Salazar AN, et al. FEMS Yeast Res. 2017 Nov 1;17(7):fox074. doi: 10.1093/femsyr/fox074. FEMS Yeast Res. 2017. PMID: 28961779 Free PMC article.
Fifteen of the 16 chromosomes, the mitochondrial genome and the 2-mum plasmid are assembled in single contigs and all but one chromosome starts or ends in a telomere repeat. ...This study demonstrates the power of long-read sequ …
Fifteen of the 16 chromosomes, the mitochondrial genome and the 2-mum plasmid are assembled in single contigs and all b …
Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences.
Gould AL, Henderson JB. Gould AL, et al. Microb Genom. 2023 Dec;9(12):001161. doi: 10.1099/mgen.0.001161. Microb Genom. 2023. PMID: 38112751 Free PMC article.
The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. ...These findings highlight …
The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one sma …
Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.
Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J, Downing T. Decano AG, et al. mSphere. 2019 May 8;4(3):e00130-19. doi: 10.1128/mSphere.00130-19. mSphere. 2019. PMID: 31068432 Free PMC article.
Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to more fragmented assemblies created with short reads alone. The long-read assemblies highlighted diverse accessory …
Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to mor …
A high-resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near-complete genome assembly.
Gardiner DM, Benfield AH, Stiller J, Stephen S, Aitken K, Liu C, Kazan K. Gardiner DM, et al. Mol Plant Pathol. 2018 Jan;19(1):217-226. doi: 10.1111/mpp.12519. Epub 2017 Jan 25. Mol Plant Pathol. 2018. PMID: 27888554 Free PMC article.
In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, together with long read scaffolding of a short read-based genome assembly, was used to give a …
In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals …
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA.
Vasquez-Gross H, Kaur S, Epstein L, Dubcovsky J. Vasquez-Gross H, et al. PLoS One. 2020 Nov 11;15(11):e0238611. doi: 10.1371/journal.pone.0238611. eCollection 2020. PLoS One. 2020. PMID: 33175843 Free PMC article.
This new assembly improved gene predictions resulting in 228 more predicted complete genes than in the initial Illumina assembly (29,178 contigs, N50 of 5 kb). ...Complete phasing of additional Pst genomes or sequencing individual …
This new assembly improved gene predictions resulting in 228 more predicted complete genes than in the initial Illumina ass …