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Oxford Nanopore MinION sequencing technology has been gaining immense importance in identification of pathogen and antimicrobial resistance, though with 10-15% error rate. Short read technologies generates high accurate genome but with multiple fragments of genome. This study proposes a novel workflow to reduce the indels resulted from MinION long read sequencing by overlaying short read sequences from IonTorrent in the clinical isolates. Best of both techniques were employed which generated highly accurate-single chromosomal microbial genomes with increase in completeness of genomes from 44.5%, 30% and 43% to 98.6%, 98.6% and 96.6% for P. aeruginosa, A. veronii and B. pertussis respectively. To the best of our knowledge, this is the first study to generate a hybrid of IonTorrent and MinION reads to obtain single chromosomal genomes. This would enable to precisely infer both structural arrangement of genes and SNP based analysis for phylogenetic information.
Pubmed ID: 30978388
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Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
View all literature mentionsA Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages.
View all literature mentionsSoftware tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
View all literature mentionsSoftware tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.
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