Memory-Efficient Assembly Using Flye

Freire, Borja; Ladra, Susana; Paramá, José R.

doi:10.1109/tcbb.2021.3108843

Cited by 22 publications

(21 citation statements)

References 52 publications

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“…85 mol%, ranging from 30.06 to 31.13 mol%. A long-read assembly of strain N18-1277 was generated using Flye 2.8.1 [32], long-read polished with Medaka v1.5.0 (https://github.com/nanoporetech/medaka) and short-read polished with Polypolish v0.5.0 [33] and polca implemented in MaSuRCA v4.0.4 [34].…”

Section: Methodsmentioning

confidence: 99%

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

et al. 2023

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Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the ‘generalist’ category (n=188), 25 % as ‘poultry specialist’ (n=83), and only a few to ‘ruminant specialist’ (n=11) or ‘wild bird’ origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.

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Section: Methodsmentioning

confidence: 99%

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

et al. 2023

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“…Flye. 2.9.1 (https://github.com/fenderglass/Flye) generated the draft assembly from the processed FASTQ reads [44]. The resulting draft assembly was then indexed and mapped against the individual reads using BWA-MEM (https://github.com/bwa-mem2/bwa-mem2) [45].…”

Section: De Novo Assembly Polishing and Annotationmentioning

confidence: 99%

Application of nanopore sequencing to identify antimicrobial resistance genes, mobile genetic elements and virulence factors in clinical isolates

Kimani,

Musundi,

Wakaba

et al. 2023

Preprint

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The global health challenge posed by the emergence of antibiotic resistance pathogen is further exacerbated in African countries by the indiscriminate use of antibiotics, poor surveillance and lack of stewardship programs. To address this issue, we employed the Oxford Nanopore Technologies (ONT) to sequence 17 clinical isolates from a referral hospital in Kenya. Our comprehensive bioinformatics approach facilitated the assembly, identification of sequence types and prediction of antimicrobial resistance genes, mobile genetic elements (plasmids and integrons) and virulence genes. Of the 17 isolates, five were A. baumannii, four E. coli, three S. haemolyticus, three were E. cloacae, while S. aureus and E. faecalis were single isolates. For the detection of AMR genes, A. baumannii isolates harbored genes such as blaOXA-23 which mediates resistance to carbapenems, E. coli and E. cloacae carried blaCTX-M-15 which confers resistance to cephalosporins and S. haemolyticus harbored blaZ, responsible for resistance against penicillins. S. aureus co-haboured mecA and blaZ genes. In addition,, various other different AMR genes to chloramphenicol, macrolides, aminoglycosides, tetracycline were also observed. For plasmid replicons, E. coli carried the most number of plasmids and shared ColRNAI_1 and IncFIB(pB171)_1_pB171 with A. baumannii and IncR_1 with E. cloacae. Many genes encoding various virulence factors including fimA-I and ompA,senB were identified in E. coli,hlgA-C and hla/hly, hlb, hld in S. aureus and efaA, ebpA-C in E. faecalis. In conclusion, most isolates contained a combination of different AMR genes harbored in plasmids and integrons and virulence genes. This study provides significant information on genetic determinants of antibiotic resistant pathogens in clinical isolates and could assist in developing strategies that improve patient treatment.

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“…In this study, the assembly of Oxford Nanopore long reads using Flye (Freire et al, 2022) resulted in a network structure containing two repetitive sequences, which may correspond to four possible conformations. A hybrid assembly of short reads and long reads was performed using Unicycler (Wick et al, 2016) to obtain a genomic structure of a loop.…”

Section: Crop Sciencementioning

confidence: 99%

Assembly and comparative analysis of the complete mitochondrial genome of Poa pratensis

Ai,

Chen,

Chen

et al. 2023

Crop Science

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Poa pratensis is a widely cultivated turf grass with strong cold and drought resistance. While the chloroplast genome of P. pratensis has been sequenced, its mitochondrial genome remains unexplored. This study assembled the mitochondrial genome of P. pratensis, revealing a total length of 447,463 bp and GC content of 44.41%. Its main structure comprises a single circular molecule. Annotation results revealed the presence of 56 genes, including 34 unique protein‐coding genes, 19 tRNA genes, and 3 rRNA genes. Additionally, we investigated codon usage bias, repeats, sequence migration and RNA editing events in the genome. Furthermore, we constructed a phylogenetic tree based on the mitochondrial genomes of P. pratensis and 20 related plants. Notably, synteny analysis results demonstrated that the mitochondrial genome of P. pratensis exhibited greater variation and more significant rearrangement than those of its close relatives. This study reports the complete mitochondrial genome of P. pratensis for the first time, providing a solid foundation for further research into the genetics of bluegrass.This article is protected by copyright. All rights reserved

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Memory-Efficient Assembly Using Flye

Cited by 22 publications

References 52 publications

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

Application of nanopore sequencing to identify antimicrobial resistance genes, mobile genetic elements and virulence factors in clinical isolates

Assembly and comparative analysis of the complete mitochondrial genome of Poa pratensis

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