NanoPack2: population-scale evaluation of long-read sequencing data

Wouter, De Coster; Rademakers, Rosa

doi:10.1093/bioinformatics/btad311

Cited by 200 publications

(73 citation statements)

References 10 publications

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“…Sequencing adaptors were simultaneously removed by specifying the “--trim_adapters” flag. The results of each Guppy run were summarized using NanoPlot v. 1.40.2 (De Coster & Rademakers, 2023). Fastq files that passed basecalling were input to Mash v. 2.2.2 (Ondov et al, 2016) to confirm there was no significant contamination in the read-level data prior to assembly.…”

Section: Methodsmentioning

confidence: 99%

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Herzog,

Wu,

Hawdon

et al. 2023

Preprint

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Parasitic nematode infections represent a significant burden of disease in impoverished populations. High prevalence of infection coupled with widespread geographic distributions means populations of parasitic nematodes likely harbor high levels of genetic diversity that are not reflected in currently available genomic resources. Comparative genomic studies of parasitic nematodes have identified novel drug and vaccine targets and yielded unprecedented insights into helminth biology, highlighting the potential of high-quality reference genomes. Few genomic resources exist for parasitic nematodes, however, and most species are represented by only a single genome. This is partly due to challenges associated with generating genomic data for these parasites. Many species are small in size and yet have relatively large and complex genomes, making their genomes difficult and expensive to sequence and assemble. Short-read sequence data has primarily been used to generate genomic data for parasitic nematodes, but whole genome assemblies based on short-read data are highly discontiguous. Recent improvements in the accuracy of Oxford Nanopore Technologies (ONT) long-read data makes it an appealing approach for improving existing reference genomes and generating novel genome assemblies from uncharacterized species. This study targets three species of parasitic nematodes to compare the current gold standard hybridde novogenome assembly approach to one that relies on long-read ONT MinION data only. Hybrid assemblies were found to be more contiguous, but nonetheless, MinION data alone were used successfully to generate highly contiguous, complete, and accurate assemblies for all species quickly and inexpensively.Significant StatementHigh quality helminth genome assemblies are invaluable tools for identifying novel drug and vaccine targets and monitoring the effectiveness of control campaigns, but generating regionally relevant reference-quality genomes from a broad diversity of populations and species can be challenging when relying on traditional approaches. This study demonstrates that Oxford Nanopore Technologies MinION long-read data alone can be used to quickly and inexpensively generate highly contiguous, complete, and accurate whole genome assemblies for parasitic nematodes. These findings highlight an accessible method for increasing the resources available for comparative helminth genomics and a path toward incorporating genomic epidemiology as a routine component of assessing control campaign effectiveness.Data Availability StatementQuality-controlled MinION and Illumina data for each species are deposited in the NCBISequence Read Archive (SRA) under the BioProject accession number XXXX. Final assemblies for each species are publicly available on WormBase ParaSite.

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Section: Methodsmentioning

confidence: 99%

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Herzog,

Wu,

Hawdon

et al. 2023

Preprint

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“…Long-read sequence quality control was performed with NanoPlot v1.41.6 [62]. Raw sequences were trimmed with NanoFilt v2.8.0 [62], with parameters -q 10 -l 300 for quality and read length, respectively. Assembly was performed using Flye v2.9.2 [63] with two approaches, (i) using default genome mode for flye (flye --nano-raw reads) and (ii) metagenome mode (flye –meta –nano-raw reads).…”

Section: Methodsmentioning

confidence: 99%

Chlamydiae as symbionts of photosynthetic dinoflagellates

Maire,

Collingro,

Tandon

et al. 2023

Preprint

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Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species,CandidatusAlgichlamydia australiensis (A. australiensisthereafter), capable of infecting the photosynthetic dinoflagellateCladocopiumsp. (originally isolated from a scleractinian coral).A. australiensiswas confirmed to be intracellular by fluorescencein situhybridization and confocal laser scanning microscopy, and temporally stable at the population level by monitoring its relative abundance across four weeks of host growth. Using a combination of short- and long-read sequencing, we recovered a high-quality (completeness 91.73% and contamination 0.27%) metagenome-assembled genome ofA. australiensis. Phylogenetic analyses show that this chlamydial taxon represents a new genus and species within the Simkaniaceae family.A. australiensispossesses all the hallmark genes for chlamydiae-host interactions, including a complete type III secretion system. In addition, a type IV secretion system is encoded on a plasmid and has previously been observed for only three other chlamydial species. Twenty orthologous groups of genes are unique toA. australiensis, one of which is structurally similar to a protein known from Cyanobacteria and Archaeplastida involved in thylakoid biogenesis and maintenance, hinting at potential chlamydiae interactions with the chloroplasts ofCladocopiumcells. DespiteCladocopiumbeing itself a symbiont of cnidarians, a meta-analysis of 12,009 cnidarian 16S rRNA gene metabarcoding samples only returned five samples withA. australiensissequences, suggestingA. australiensisdoes not associate with cnidarians. Our study shows that chlamydiae infect dinoflagellate symbionts of cnidarians, the first photosynthetic organism reported to harbor chlamydiae, thereby expanding the breadth of chlamydial hosts and providing a new contribution to the discussion around the role of chlamydiae in the establishment of the primary plastid.

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“…FastQ reads were quality assessed using FastQC (version 0.11.9) [7] and trimmed using FastP (version 0.20.1) [8] for Illumina or using Chopper (version 0.5.0) [9] for Oxford Nanopore outputs. De novo genome assemblies were generated using SPAdes (version 3.12.0) [10] for short reads and genome assembly for long reads was carried out using Flye (version 2.9.2) [11] obtaining 37 and one contig, respectively, with an average G+C content of 66.1 mol%.…”

Section: Data Processing Annotation and Phylogenetic Analysismentioning

confidence: 99%

Stenotrophomonas riyadhensis sp. nov., isolated from a hospital floor swab

Macori,

Al-Qahtani,

Koolman

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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During the analysis of a collection of Pseudomonas strains linked to an outbreak in an intensive care unit at King Faisal Specialist Hospital and Research Center in 2019, one isolate (CFS3442T) was identified phenotypically as Pseudomonas aeruginosa. However, whole-genome sequencing revealed its true identity as a member of the genus Stenotrophomonas, distinct from both P. aeruginosa and Stenotrophomonas maltophilia. The isolate demonstrated: (i) a significant phylogenetic distance from P. aeruginosa; (ii) considerable genomic differences from several S. maltophilia reference strains and other Stenotrophomonas species; and (iii) unique phenotypic characteristics. Based on the combined geno- and phenotypic data, we propose that this isolate represents a novel species within the genus Stenotrophomonas, for which the name Stenotrophomonas riyadhensis sp. nov. is proposed. The type strain is CFS3442T (=NCTC 14921T=LMG 33162T).

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NanoPack2: population-scale evaluation of long-read sequencing data

Cited by 200 publications

References 10 publications

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Chlamydiae as symbionts of photosynthetic dinoflagellates

Stenotrophomonas riyadhensis sp. nov., isolated from a hospital floor swab

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