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Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

https://doi.org/10.1101/215707
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2015.10.009openalex-snapshot
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
inferredcites →https://doi.org/10.1016/j.tig.2017.05.005openalex-snapshot
Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/ncomms7717openalex-snapshot
Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
inferredcites →https://doi.org/10.1073/pnas.0409727102openalex-snapshot
Genomic insights that advance the species definition for prokaryotes
inferredcites →https://doi.org/10.1093/bioinformatics/btu641openalex-snapshot
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
inferredcites →https://doi.org/10.1093/bioinformatics/btu745openalex-snapshot
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1101/027607openalex-snapshot
One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification
inferredcites →https://doi.org/10.1101/050559openalex-snapshot
MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman
inferredcites →https://doi.org/10.1101/072082openalex-snapshot
panX: pan-genome analysis and exploration
inferredcites →https://doi.org/10.1101/105759openalex-snapshot
Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica
inferredcites →https://doi.org/10.1101/gr.201863.115openalex-snapshot
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot
Centrifuge: rapid and sensitive classification of metagenomic sequences
inferredcites →https://doi.org/10.1126/science.aad2545openalex-snapshot
The 5300-year-old Helicobacter pylori genome of the Iceman
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot
Mash: fast genome and metagenome distance estimation using MinHash
inferredcites →https://doi.org/10.1186/s13059-017-1299-7openalex-snapshot
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
inferredcites →https://doi.org/10.1186/s13059-017-1309-9openalex-snapshot
DESMAN: a new tool for de novo extraction of strains from metagenomes
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0089142openalex-snapshot
A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.quaint.2020.11.019openalex-snapshot
Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus
inferred← citeshttps://doi.org/10.1079/cabireviews.2024.0011openalex-snapshot
Multiple approaches in the study of ancient human microbiome
inferred← citeshttps://doi.org/10.1080/22221751.2025.2562053openalex-snapshot
Post-COVID-19 disruption of the respiratory microbiome modulates Mycoplasma pneumoniae : a multi-center retrospective investigation study
inferred← citeshttps://doi.org/10.1093/nar/gkaf118openalex-snapshot
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses
inferred← citeshttps://doi.org/10.1101/2020.09.06.284828openalex-snapshot
Metagenomics Strain Resolution on Assembly Graphs
inferred← citeshttps://doi.org/10.1186/s13059-019-1903-0openalex-snapshot
HOPS: automated detection and authentication of pathogen DNA in archaeological remains
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