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Keywords {🔍}

reference, strains, strain, samples, genome, strainge, sample, straingst, straingr, genomes, coli, database, fig, metagenomic, article, coverage, set, data, acni, single, google, scholar, tools, species, reads, references, midas, additional, allele, threshold, file, tool, similarity, kmers, present, read, including, low, escherichia, ani, pairs, reported, abundance, kmer, metagenomes, bacterial, related, matching, strong, predicted,

Topics {✒️}

}_j}\frac{c_i}{d_{ij}}$$ time-consuming phylogenomic pipelines strain-level microbial detection short-read metagenomic sequencing complex microbial communities include k-mer counts short-read sequencing data builtin prepare-ref tool full size image high-quality supporting reads recover strain-level variation high-quality reference genomes dissecting strain-level diversity plot precision-recall curves microbial communities comprise excluding multi-mappable regions �multi-mappable” read alignments sample k-mer counts jaccard k-mer similarity population genetics popular strain-tracking tool tool called prepare-ref real-world sample sets studying strain-level variation discern strain-level variation article download pdf single-copy core phylogeny healthy human microbiome low abundant uti-causing mother-baby strain sharing single uti-causing strain database k-mers remaining privacy choices/manage cookies k-mer based tool k-mer set ksample gene-level differences metagenomics strain resolution stacked barplot showing identify single-nucleotide variants ultra-sensitive detection infant gut microbiome full access $${\lambda}_j=\frac{1}{\mid { urinary tract infections base quality scores characterize low-abundance strains long-time gut carriage escherichia-specific reference database metagenome shotgun sequenced de novo extraction

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         description:Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.
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            name:Delft University of Technology
            address:
               name:Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
               type:PostalAddress
            type:Organization
      name:Ashlee M. Earl
      url:http://orcid.org/0000-0001-7857-9145
      affiliation:
            name:Broad Institute
            address:
               name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Applied Invention, Cambridge, USA
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA
      name:Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, USA
      name:Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
      name:Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, USA
      name:Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, USA
      name:Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA
      name:Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, USA
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA
      name:Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
      name:Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA

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