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Field-based species identification in eukaryotes using real-time nanopore sequencing

https://doi.org/10.1101/107656
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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.bdq.2015.02.001openalex-snapshot
Assessing the performance of the Oxford Nanopore Technologies MinION
inferredcites →https://doi.org/10.1038/nature16996openalex-snapshot
Real-time, portable genome sequencing for Ebola surveillance
inferredcites →https://doi.org/10.1038/ng.3617openalex-snapshot
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
inferredcites →https://doi.org/10.1038/ng.807openalex-snapshot
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
inferredcites →https://doi.org/10.1038/s41598-017-07650-6openalex-snapshot
Rapid de novo assembly of the European eel genome from nanopore sequencing reads
inferredcites →https://doi.org/10.1073/pnas.0905845106openalex-snapshot
A DNA barcode for land plants
inferredcites →https://doi.org/10.1073/pnas.1209160109openalex-snapshot
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1073/pnas.93.24.13770openalex-snapshot
Characterization of individual polynucleotide molecules using a membrane channel
inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot
ROCR: visualizing classifier performance in R
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv688openalex-snapshot
hybrid SPA des : an algorithm for hybrid assembly of short and long reads
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/jac/dkw397openalex-snapshot
Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkr1090openalex-snapshot
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
inferredcites →https://doi.org/10.1093/nar/gkt1376openalex-snapshot
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis
inferredcites →https://doi.org/10.1098/rstb.2015.0124openalex-snapshot
A trip down memory lane about sex differences in the brain
inferredcites →https://doi.org/10.1098/rstb.2015.0330openalex-snapshot
A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
inferredcites →https://doi.org/10.1098/rstb.2015.0335openalex-snapshot
Multilocus inference of species trees and DNA barcoding
inferredcites →https://doi.org/10.1098/rstb.2015.0338openalex-snapshot
Telling plant species apart with DNA: from barcodes to genomes
inferredcites →https://doi.org/10.1101/013490openalex-snapshot
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
inferredcites →https://doi.org/10.1101/073965openalex-snapshot
In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota
inferredcites →https://doi.org/10.1101/084772openalex-snapshot
The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.113985.110openalex-snapshot
Adaptive seeds tame genomic sequence comparison
inferredcites →https://doi.org/10.1101/gr.191692.115openalex-snapshot
A vision for ubiquitous sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12046openalex-snapshot
The seven deadly sins of DNA barcoding
inferredcites →https://doi.org/10.1111/1755-0998.12324openalex-snapshot
A first look at the Oxford Nanopore MinION sequencer
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05235.xopenalex-snapshot
A fuzzy‐set‐theory‐based approach to analyse species membership in DNA barcoding
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-5-59openalex-snapshot
Gene finding in novel genomes
inferredcites →https://doi.org/10.1186/s13073-016-0356-2openalex-snapshot
Mobile real-time surveillance of Zika virus in Brazil
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0020552openalex-snapshot
DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

What points at this work

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

inferred← citeshttps://doi.org/10.1093/mollus/eyy052zenodo-depositor-declared
Bringing the lab to the field: a new lowlandMicroparmarionsemi-slug (Gastropoda: Ariophantidae) described and DNA-barcoded in the forest
inferred← citeshttps://doi.org/10.1038/s41598-017-03996-zopenalex-snapshot
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000251openalex-snapshot
A 3D-printed hand-powered centrifuge for molecular biology
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