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Top Articles

1SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignmentsMicrobial Genomics2016888
2Completing bacterial genome assemblies with multiplex MinION sequencingMicrobial Genomics2017559
3ARIBA: rapid antimicrobial resistance genotyping directly from sequencing readsMicrobial Genomics2017478
4Microreact: visualizing and sharing data for genomic epidemiology and phylogeographyMicrobial Genomics2016470
5Identification of Klebsiella capsule synthesis loci from whole genome dataMicrobial Genomics2016372
6MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assembliesMicrobial Genomics2018349
7ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotypingMicrobial Genomics2018307
8NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formatsMicrobial Genomics2016237
9Genome-scale rates of evolutionary change in bacteriaMicrobial Genomics2016224
10Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumanniiMicrobial Genomics2019209
11Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina dataMicrobial Genomics2016208
12chewBBACA: A complete suite for gene-by-gene schema creation and strain identificationMicrobial Genomics2018201
13On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing dataMicrobial Genomics2017198
14Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populationsMicrobial Genomics2018197
15The diversity of Klebsiella pneumoniae surface polysaccharidesMicrobial Genomics2016185
16CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology communityMicrobial Genomics2016176
17EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogensMicrobial Genomics2015174
18Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomesMicrobial Genomics2019171
19Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identificationMicrobial Genomics2021168
20Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic FirmicutesMicrobial Genomics2016162
21Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1Microbial Genomics2016155
22ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypesMicrobial Genomics2022126
23Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 cloneMicrobial Genomics2017122
24mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single speciesMicrobial Genomics2018121
25Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK BiobankMicrobial Genomics2020120
26SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiologyMicrobial Genomics2017119
27Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with KaptiveMicrobial Genomics2020118
28In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineagesMicrobial Genomics2016110
29Expanding an expanded genome: long-read sequencing of Trypanosoma cruziMicrobial Genomics2018110
30Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UKMicrobial Genomics2015105
31Trends in fluoroquinolone resistance in CampylobacterMicrobial Genomics2018100
32The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transferMicrobial Genomics201699
33Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophagesMicrobial Genomics201895
34Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulenceMicrobial Genomics201891
35Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26Microbial Genomics201789
36Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogensMicrobial Genomics201688
37Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scoresMicrobial Genomics202087
38Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationshipsMicrobial Genomics201586
39Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensalMicrobial Genomics201786
40Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencingMicrobial Genomics201880
41Quantitative assessment of insertion sequence impact on bacterial genome architectureMicrobial Genomics201680
42Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approachesMicrobial Genomics201774
43Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary historyMicrobial Genomics202171
44Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198Microbial Genomics201969
45Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory studyMicrobial Genomics202069
46Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analysesMicrobial Genomics202069
47SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence dataMicrobial Genomics201868
48Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmidMicrobial Genomics202068
49Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution networkMicrobial Genomics201667
50Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillanceMicrobial Genomics202067