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A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing

https://doi.org/10.1101/752774
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer
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Assessing Gut Microbial Diversity from Feces and Rectal Mucosa
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Application of MALDI-TOF for Bacterial Identification
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The Human Microbiome and Obesity: Moving beyond Associations
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Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases
inferredcites →https://doi.org/10.1016/j.mimet.2006.05.009openalex-snapshot
16S rRNA sequencing in routine bacterial identification: A 30-month experiment
inferredcites →https://doi.org/10.1016/j.ygeno.2015.11.003openalex-snapshot
The sequence of sequencers: The history of sequencing DNA
inferredcites →https://doi.org/10.1016/j.ympev.2014.02.013openalex-snapshot
Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1021/ac00120a026openalex-snapshot
Use of Non-Cross-Linked Polyacrylamide for Four-Color DNA Sequencing by Capillary Electrophoresis Separation of Fragments up to 640 Bases in Length in Two Hours
inferredcites →https://doi.org/10.1080/14789450.2017.1282825openalex-snapshot
Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives
inferredcites →https://doi.org/10.1080/14789450.2018.1499469openalex-snapshot
Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/gigascience/giy033openalex-snapshot
Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
inferredcites →https://doi.org/10.1093/gigascience/giy140openalex-snapshot
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
inferredcites →https://doi.org/10.1093/gigascience/giz043openalex-snapshot
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msw088openalex-snapshot
RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics
inferredcites →https://doi.org/10.1093/nar/16.22.10881openalex-snapshot
Multiple sequence alignment with hierarchical clustering
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1101/645903openalex-snapshot
Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.5661407openalex-snapshot
A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
inferredcites →https://doi.org/10.1111/1755-0998.12890openalex-snapshot
A Min ION ™‐based pipeline for fast and cost‐effective DNA barcoding
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/jcm.01228-07openalex-snapshot
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
inferredcites →https://doi.org/10.1128/jcm.01463-10openalex-snapshot
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry as an Alternative to 16S rRNA Gene Sequencing for Identification of Difficult-To-Identify Bacterial Strains
inferredcites →https://doi.org/10.1128/jcm.38.10.3623-3630.2000openalex-snapshot
16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates
inferredcites →https://doi.org/10.1128/jcm.41.5.1996-2001.2003openalex-snapshot
Usefulness of the MicroSeq 500 16S Ribosomal DNA-Based Bacterial Identification System for Identification of Clinically Significant Bacterial Isolates with Ambiguous Biochemical Profiles
inferredcites →https://doi.org/10.1186/s12859-015-0692-zopenalex-snapshot
leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences
inferredcites →https://doi.org/10.1186/s12866-019-1500-0openalex-snapshot
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
inferredcites →https://doi.org/10.1186/s13742-016-0111-zopenalex-snapshot
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
inferredcites →https://doi.org/10.1371/journal.pone.0106303openalex-snapshot
Comparison of the Bruker MALDI-TOF Mass Spectrometry System and Conventional Phenotypic Methods for Identification of Gram-Positive Rods
inferredcites →https://doi.org/10.1371/journal.pone.0117617openalex-snapshot
Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens
inferredcites →https://doi.org/10.1371/journal.pone.0144878openalex-snapshot
A Side by Side Comparison of Bruker Biotyper and VITEK MS: Utility of MALDI-TOF MS Technology for Microorganism Identification in a Public Health Reference Laboratory
inferredcites →https://doi.org/10.1371/journal.pone.0163962openalex-snapshot
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
inferredcites →https://doi.org/10.1371/journal.pone.0184741openalex-snapshot
On site DNA barcoding by nanopore sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0218077openalex-snapshot
Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification
inferredcites →https://doi.org/10.3389/fmicb.2018.02225openalex-snapshot
Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk
inferredcites →https://doi.org/10.3390/genes10060468openalex-snapshot
A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field
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