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plasmidSPAdes: assembling plasmids from whole genome sequencing data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1073/pnas.1116410109openalex-snapshot
Insights into the bovine rumen plasmidome
inferredcites →https://doi.org/10.1073/pnas.1514326112openalex-snapshot
Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btr011openalex-snapshot
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btu266openalex-snapshot
ExSPAnder: a universal repeat resolver for DNA fragment assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btw651openalex-snapshot
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
inferredcites →https://doi.org/10.1093/gbe/evv244openalex-snapshot
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
inferredcites →https://doi.org/10.1101/gr.2395204openalex-snapshot
De Novo Repeat Classification and Fragment Assembly
inferredcites →https://doi.org/10.1126/science.aac4812openalex-snapshot
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
inferredcites →https://doi.org/10.1126/scitranslmed.3009845openalex-snapshot
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae
inferredcites →https://doi.org/10.1128/aac.02412-14openalex-snapshot
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
inferredcites →https://doi.org/10.1128/aem.00354-06openalex-snapshot
Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing
inferredcites →https://doi.org/10.1128/jb.151.1.462-464.1982openalex-snapshot
Transformation of Saccharomyces cerevisiae with linear DNA killer plasmids from Kluyveromyces lactis
inferredcites →https://doi.org/10.1128/microbiolspec.plas-0031-2014openalex-snapshot
Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Escherichia coli Plasmids
inferredcites →https://doi.org/10.1186/1471-2148-13-1openalex-snapshot
New approaches for unravelling reassortment pathways
inferredcites →https://doi.org/10.1186/1471-2148-13-262openalex-snapshot
Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group
inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot
The RAST Server: Rapid Annotations using Subsystems Technology
inferredcites →https://doi.org/10.1371/journal.pgen.1004766openalex-snapshot
Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
inferredcites →https://doi.org/10.3389/fmicb.2015.00242openalex-snapshot
Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy
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Sequencing Strategy to Ensure Accurate Plasmid Assembly
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inferred← citeshttps://doi.org/10.1038/s41467-025-59229-9openalex-snapshot
HiBC: a publicly available collection of bacterial strains isolated from the human gut
inferred← citeshttps://doi.org/10.1038/s41576-019-0108-4openalex-snapshot
Sequencing-based methods and resources to study antimicrobial resistance
inferred← citeshttps://doi.org/10.1038/s41576-024-00746-6openalex-snapshot
Sequencing-based analysis of microbiomes
inferred← citeshttps://doi.org/10.1038/s41598-017-18659-2openalex-snapshot
Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses
inferred← citeshttps://doi.org/10.1038/s41598-018-25474-wopenalex-snapshot
Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis
inferred← citeshttps://doi.org/10.1038/s41598-019-42122-zopenalex-snapshot
Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden
inferred← citeshttps://doi.org/10.1038/s41598-020-74033-9openalex-snapshot
Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales
inferred← citeshttps://doi.org/10.1038/s41598-022-17835-3openalex-snapshot
Staphylococcus aureus lineages associated with a free-ranging population of the fruit bat Pteropus livingstonii retained over 25 years in captivity
inferred← citeshttps://doi.org/10.1038/s41598-022-23690-zopenalex-snapshot
Examining the impact of zinc on horizontal gene transfer in Enterobacterales
inferred← citeshttps://doi.org/10.1038/s41598-022-24735-zopenalex-snapshot
Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate
inferred← citeshttps://doi.org/10.1038/s41598-022-26005-4openalex-snapshot
Comprehensive analysis of the metabolic and genomic features of tannin-transforming Lactiplantibacillus plantarum strains
inferred← citeshttps://doi.org/10.1038/s41598-023-37176-zopenalex-snapshot
Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential
inferred← citeshttps://doi.org/10.1038/s41598-023-46638-3openalex-snapshot
Identification of a unique conserved region from a kinetoplastid genome of Leishmania orientalis (formerly named Leishmania siamensis) strain PCM2 in Thailand
inferred← citeshttps://doi.org/10.1038/s41598-024-51819-9openalex-snapshot
Genomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh
inferred← citeshttps://doi.org/10.1038/s41598-024-70977-4openalex-snapshot
First insight into the whole genome sequence variations in clarithromycin resistant Helicobacter pylori clinical isolates in Russia
inferred← citeshttps://doi.org/10.1038/s41598-024-73703-2openalex-snapshot
The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species
inferred← citeshttps://doi.org/10.1038/s41598-024-78564-3openalex-snapshot
Whole genome analysis of 26 bacterial strains reveals aromatic and hydrocarbon degrading enzymes from diverse environmental soil samples
inferred← citeshttps://doi.org/10.1038/s41598-025-25044-xopenalex-snapshot
Comparative genomics uncovers adaptive and biotechnological potential of Enterobacter xiangfangensis MDMC82 isolated from desert, and highlights putative core Enterobacteriaceae functions
inferred← citeshttps://doi.org/10.1038/s41598-026-35600-8openalex-snapshot
Complete genome sequence and functional characterization of Bacillus amyloliquefaciens NJF-55: a sheep-derived probiotic candidate
inferred← citeshttps://doi.org/10.1038/s44259-025-00154-8openalex-snapshot
Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment
inferred← citeshttps://doi.org/10.1038/srep40694openalex-snapshot
Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae
inferred← citeshttps://doi.org/10.1038/srep43555openalex-snapshot
Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China
inferred← citeshttps://doi.org/10.1039/d0ra01484bopenalex-snapshot
Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design
inferred← citeshttps://doi.org/10.1080/14620316.2021.1973583openalex-snapshot
Virome analysis for identification of viruses associated with asymptomatic infection of purple passion fruit (Passiflora edulis f. edulis) in Colombia
inferred← citeshttps://doi.org/10.1080/17460913.2025.2492472openalex-snapshot
Deciphering probiotic potential: a comprehensive guide to probiogenomic analyses
inferred← citeshttps://doi.org/10.1080/20477724.2019.1574112openalex-snapshot
Extensive drug resistant Salmonella enterica serovar Senftenberg carrying blaNDM encoding plasmid p5558 (IncA/C) from India
inferred← citeshttps://doi.org/10.1080/20477724.2025.2513769openalex-snapshot
Coriander borne Salmonella superbug: genomic assessments of chromosomal and plasmid-associated resistance, virulence and MGEs of XDR Salmonella enterica Typhi NH1
inferred← citeshttps://doi.org/10.1080/20477724.2025.2610657openalex-snapshot
Genomic characterization of Legionella pneumophila serogroup 1 ST901 isolates responsible for recurrent travel-associated Legionnaires’ disease cases and clusters
inferred← citeshttps://doi.org/10.1080/22221751.2020.1733439openalex-snapshot
Emerging colistin resistance in Salmonella enterica serovar Newport isolates from human infections
inferred← citeshttps://doi.org/10.1080/22221751.2025.2539193openalex-snapshot
Whole-genome analysis of NDM-producing Providencia hangzhouensis associated with recurrent bacteraemia with rapid development of aztreonam-avibactam resistance
inferred← citeshttps://doi.org/10.1080/23802359.2022.2048214openalex-snapshot
The complete chloroplast genome ofTilia endochryseaHandel-Mazzetti 1926 (Malvaceae)
inferred← citeshttps://doi.org/10.1080/24701394.2024.2439433openalex-snapshot
When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats’ species (Felidae: Machairodontinae)
inferred← citeshttps://doi.org/10.1089/fpd.2023.0118openalex-snapshot
In Silico Detection of Integrons and Their Relationship with Resistance Phenotype of Salmonella Isolates from a Brazilian Pork Production Chain
inferred← citeshttps://doi.org/10.1093/bib/bbaa059openalex-snapshot
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
inferred← citeshttps://doi.org/10.1093/bib/bbaf589openalex-snapshot
Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species
inferred← citeshttps://doi.org/10.1093/bib/bbx162openalex-snapshot
Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa233openalex-snapshot
gplas: a comprehensive tool for plasmid analysis using short-read graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa490openalex-snapshot
Metaviral SPAdes : assembly of viruses from metagenomic data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab719openalex-snapshot
WGA-LP: a pipeline for whole genome assembly of contaminated reads
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad250openalex-snapshot
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae299openalex-snapshot
PlasCAT: Plasmid Cloud Assembly Tool
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw651openalex-snapshot
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz413openalex-snapshot
HyAsP, a greedy tool for plasmids identification
inferred← citeshttps://doi.org/10.1093/clinchem/hvaa172openalex-snapshot
Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes!
inferred← citeshttps://doi.org/10.1093/femsec/fix152openalex-snapshot
Lactobacillus backii and Pediococcus damnosus isolated from 170-year-old beer recovered from a shipwreck lack the metabolic activities required to grow in modern lager beer
inferred← citeshttps://doi.org/10.1093/gbe/evx001openalex-snapshot
Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems
inferred← citeshttps://doi.org/10.1093/jac/dkaa398openalex-snapshot
Characterization of carbapenemase-producingSerratia marcescensand whole-genome sequencing for plasmid typing in a hospital in Madrid, Spain (2016–18)
inferred← citeshttps://doi.org/10.1093/jac/dkaf028openalex-snapshot
One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings
inferred← citeshttps://doi.org/10.1093/jac/dkw318openalex-snapshot
WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidalSalmonella
inferred← citeshttps://doi.org/10.1093/jac/dky111openalex-snapshot
Novel plasmid-mediated colistin resistance gene mcr-7.1 in Klebsiella pneumoniae
inferred← citeshttps://doi.org/10.1093/jac/dky446openalex-snapshot
Detection and characterization of ESBL-producingEscherichia coliexpressingmcr-1from dairy cows in China
inferred← citeshttps://doi.org/10.1093/jac/dkz097openalex-snapshot
Emergence of optrA-mediated linezolid resistance in enterococci from France, 2006–16
inferred← citeshttps://doi.org/10.1093/jac/dkz550openalex-snapshot
Klebsiella pneumoniae ST307 with OXA-181: threat of a high-risk clone and promiscuous plasmid in a resource-constrained healthcare setting
inferred← citeshttps://doi.org/10.1093/jacamr/dlae050openalex-snapshot
Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization
inferred← citeshttps://doi.org/10.1093/jambio/lxac027openalex-snapshot
Genomic features and heat resistance profiles ofEscherichia coliisolated from Brazilian beef
inferred← citeshttps://doi.org/10.1093/molbev/msaa235openalex-snapshot
Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks
inferred← citeshttps://doi.org/10.1093/molbev/msy027openalex-snapshot
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades
inferred← citeshttps://doi.org/10.1093/nar/gkaa700openalex-snapshot
Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi
inferred← citeshttps://doi.org/10.1093/nar/gkaa727openalex-snapshot
Rapid, robust plasmid verification by de novo assembly of short sequencing reads
inferred← citeshttps://doi.org/10.1093/nar/gkab1111openalex-snapshot
PLSDB: advancing a comprehensive database of bacterial plasmids
inferred← citeshttps://doi.org/10.1093/nar/gkab1115openalex-snapshot
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes
inferred← citeshttps://doi.org/10.1093/nar/gkad578openalex-snapshot
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
inferred← citeshttps://doi.org/10.1093/nar/gkx1321openalex-snapshot
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
inferred← citeshttps://doi.org/10.1093/nar/gky1073openalex-snapshot
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data
inferred← citeshttps://doi.org/10.1093/nar/gky726openalex-snapshot
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats
inferred← citeshttps://doi.org/10.1093/nargab/lqab071openalex-snapshot
CONSULT: accurate contamination removal using locality-sensitive hashing
inferred← citeshttps://doi.org/10.1093/nargab/lqab096openalex-snapshot
pLS20 is the archetype of a new family of conjugative plasmids harboured byBacillusspecies
inferred← citeshttps://doi.org/10.1093/nargab/lqad066openalex-snapshot
Mge-cluster: a reference-free approach for typing bacterial plasmids
inferred← citeshttps://doi.org/10.1093/nargab/lqag028openalex-snapshot
gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species
inferred← citeshttps://doi.org/10.1094/phyto-02-23-0077-scopenalex-snapshot
A Brief Evaluation of a Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen Xanthomonas euvesicatoria pv. perforans
inferred← citeshttps://doi.org/10.1098/rstb.2021.0245openalex-snapshot
The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies
inferred← citeshttps://doi.org/10.1099/acmi.0.000429openalex-snapshot
Plasmids of the urinary microbiota
inferred← citeshttps://doi.org/10.1099/acmi.0.000468.v3openalex-snapshot
Evaluation of five commercial DNA extraction kits using Salmonella as a model for implementation of rapid Nanopore sequencing in routine diagnostic laboratories
inferred← citeshttps://doi.org/10.1099/acmi.0.000986.v4openalex-snapshot
Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand
inferred← citeshttps://doi.org/10.1099/ijsem.0.004715openalex-snapshot
Closed genome sequences of Staphylococcus lloydii sp. nov. and Staphylococcus durrellii sp. nov. isolated from captive fruit bats (Pteropus livingstonii)
inferred← citeshttps://doi.org/10.1099/jmm.0.000882openalex-snapshot
Characterization of a colistin-resistant Avian Pathogenic Escherichia coli ST69 isolate recovered from a broiler chicken in Germany
inferred← citeshttps://doi.org/10.1099/jmm.0.001922openalex-snapshot
Genomic epidemiology and resistant genes of Acinetobacter baumannii clinical strains in Vietnamese hospitals
inferred← citeshttps://doi.org/10.1099/mgen.0.000118openalex-snapshot
Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches
inferred← citeshttps://doi.org/10.1099/mgen.0.000128openalex-snapshot
On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
inferred← citeshttps://doi.org/10.1099/mgen.0.000164openalex-snapshot
PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data
inferred← citeshttps://doi.org/10.1099/mgen.0.000191openalex-snapshot
Genome analysis of methicillin resistance in Macrococcus caseolyticus from dairy cattle in England and Wales
inferred← citeshttps://doi.org/10.1099/mgen.0.000206openalex-snapshot
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
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