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Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION TM sequencing

https://doi.org/10.1101/019356

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What this work says

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

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Software Tools and Algorithms for Biological Systems

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Advances in Knowledge Discovery and Data Mining

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Finite-state models in the alignment of macromolecules

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Parametric optimization of sequence alignment

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The Next-Generation Sequencing Revolution and Its Impact on Genomics

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A formal theory of inductive inference. Part I

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Basic Local Alignment Search Tool

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The potential and challenges of nanopore sequencing

inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

inferredcites →https://doi.org/10.1038/ncomms10063openalex-snapshot

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

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Metagenomic microbial community profiling using unique clade-specific marker genes

inferredcites →https://doi.org/10.1038/nmeth.3290openalex-snapshot

Improved data analysis for the MinION nanopore sequencer

inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot

A complete bacterial genome assembled de novo using only nanopore sequencing data

inferredcites →https://doi.org/10.1038/nrg3624openalex-snapshot

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

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Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

inferredcites →https://doi.org/10.1073/pnas.1322678111openalex-snapshot

Global dissemination of a multidrug resistant Escherichia coli clone

inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot

Amino acid substitution matrices from protein blocks.

inferredcites →https://doi.org/10.1073/pnas.93.24.13770openalex-snapshot

Characterization of individual polynucleotide molecules using a membrane channel

inferredcites →https://doi.org/10.1073/pnas.95.6.3140openalex-snapshot

Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms

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Simultaneous Confidence Intervals and Sample Size Determination for Multinomial Proportions

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv658openalex-snapshot

Realtime analysis and visualization of MinION sequencing data with npReader

inferredcites →https://doi.org/10.1093/bioinformatics/btw569openalex-snapshot

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

inferredcites →https://doi.org/10.1093/comjnl/11.2.185openalex-snapshot

An Information Measure for Classification

inferredcites →https://doi.org/10.1093/jac/dks261openalex-snapshot

Identification of acquired antimicrobial resistance genes

inferredcites →https://doi.org/10.1093/jac/dkv206openalex-snapshot

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

inferredcites →https://doi.org/10.1093/nar/gkn1006openalex-snapshot

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

inferredcites →https://doi.org/10.1101/030742openalex-snapshot

What’s in my pot? Real-time species identification on the MinION™

inferredcites →https://doi.org/10.1109/dcc.2007.7openalex-snapshot

A Simple Statistical Algorithm for Biological Sequence Compression

inferredcites →https://doi.org/10.1126/science.1237619openalex-snapshot

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

inferredcites →https://doi.org/10.1128/aac.03900-14openalex-snapshot

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

inferredcites →https://doi.org/10.1128/jcm.00066-13openalex-snapshot

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

inferredcites →https://doi.org/10.1128/jcm.02452-13openalex-snapshot

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

inferredcites →https://doi.org/10.1128/jcm.06094-11openalex-snapshot

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

inferredcites →https://doi.org/10.1128/jcm.43.8.4178-4182.2005openalex-snapshot

Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates

inferredcites →https://doi.org/10.1145/1083784.1083789openalex-snapshot

Mining data streams

inferredcites →https://doi.org/10.1186/1471-2105-11-599openalex-snapshot

A genome alignment algorithm based on compression

inferredcites →https://doi.org/10.1186/1471-2105-11-80openalex-snapshot

Parameters for accurate genome alignment

inferredcites →https://doi.org/10.1186/2047-217x-3-22openalex-snapshot

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

inferredcites →https://doi.org/10.1186/s13059-015-0677-2openalex-snapshot

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

inferredcites →https://doi.org/10.1186/s13742-015-0051-zopenalex-snapshot

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

inferredcites →https://doi.org/10.1371/journal.pone.0099209openalex-snapshot

Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

inferredcites →https://doi.org/10.1561/0400000002openalex-snapshot

Data Streams: Algorithms and Applications

What points at this work

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

inferred← citeshttps://doi.org/10.1038/ncomms11307openalex-snapshot

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

inferred← citeshttps://doi.org/10.1038/ncomms14515openalex-snapshot

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

inferred← citeshttps://doi.org/10.1093/bioinformatics/btv658openalex-snapshot

Realtime analysis and visualization of MinION sequencing data with npReader

inferred← citeshttps://doi.org/10.1101/019281openalex-snapshot

Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

inferred← citeshttps://doi.org/10.1177/2472630317727519openalex-snapshot

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

inferred← citeshttps://doi.org/10.1186/s13073-016-0326-8openalex-snapshot

Next-generation sequencing diagnostics of bacteremia in septic patients

inferred← citeshttps://doi.org/10.1186/s13742-016-0137-2openalex-snapshot

Streaming algorithms for identification pathogens and antibiotic resistance potential from real-time MinION™ sequencing

inferred← citeshttps://doi.org/10.70675/5b4b55e3zaf2fz483ez9460z4ba0c7632874openalex-snapshot

Développement d’outils innovants pour l'étude de l’infection chronique

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