Research graph
References from Sub-consensus haploid variant calling in long-read sequencing technology. Local targets link to admitted publications; unresolved targets remain external evidence.
Global landscape of SARS-CoV-2 genomic surveillance and data sharing
10.1038/s41588-022-01033-y · 2022 · External reference
Next-generation sequencing of infectious pathogens
10.1001/jama.2018.21669 · 2019 · External reference
SARS-CoV-2: Evolution and emergence of new viral variants
10.3390/v14040653 · 2022 · External reference
Bioinformatics resources for SARS-CoV-2 discovery and surveillance
10.1093/bib/bbaa386 · 2021 · External reference
Virus variants: GISAID policies incentivize surveillance in global south
10.1038/d41586-021-01310-6 · 2021 · External reference
The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity
10.1002/jmv.28138 · 2023 · External reference
Traceability of SARS-CoV-2 transmission through quasispecies analysis
10.1002/jmv.28848 · 2023 · External reference
A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
10.1093/bib/bbz086 · 2020 · External reference
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
10.1093/bioinformatics/btab846 · 2022 · External reference
Advancements in detection of SARS-CoV-2 infection for confronting COVID-19 pandemics
2021 · External reference
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
10.1038/ncomms11307 · 2016 · External reference
A general approach to identify low-frequency variants within influenza samples collected during routine surveillance
2022 · External reference
Strategy and Performance evaluation of low-frequency variant calling for SARS-CoV-2 using targeted deep illumina sequencing
10.3389/fmicb.2021.747458 · 2021 · External reference
Patterns of within-host genetic diversity in SARS-CoV-2
10.7554/elife.66857 · 2021 · External reference
Nanopore technology and its applications in gene sequencing
10.3390/bios11070214 · 2021 · External reference
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
10.1186/s13059-018-1462-9 · 2018 · External reference
Error analysis of idealized nanopore sequencing: Nanoanalysis
10.1002/elps.201300174 · 2013 · External reference
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols
10.1371/journal.pone.0259277 · 2021 · External reference
Identification of genomic variants of SARS-CoV-2 using nanopore sequencing
10.3390/medicina58121841 · 2022 · External reference
Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses
10.1016/j.ygeno.2021.03.018 · 2021 · External reference
Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads
2024 · External reference
Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis
10.1038/s41598-021-00178-w · 2021 · External reference
Multiple occurrences of a 168-nucleotide deletion in SARS-CoV-2 ORF8, unnoticed by standard amplicon sequencing and variant calling pipelines
10.3390/v13091870 · 2021 · External reference
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
10.1038/s41467-020-20075-6 · 2020 · External reference
Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
10.1186/s13059-022-02751-6 · 2022 · External reference
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
10.1186/s13059-021-02510-z · 2021 · External reference
Symphonizing pileup and full-alignment for deep learning-based long-read variant calling
10.1038/s43588-022-00387-x · 2022 · External reference
A universal SNP and small-indel variant caller using deep neural networks
10.1038/nbt.4235 · 2018 · External reference
Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing
10.1038/s41467-019-12493-y · 2019 · External reference
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
10.1186/s13059-018-1618-7 · 2019 · External reference
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
10.1093/nar/gks918 · 2012 · External reference
Sequencing of SARS-CoV-2 genome using different nanopore chemistries
10.1007/s00253-021-11250-w · 2021 · External reference
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
10.1038/s41467-022-28852-1 · 2022 · External reference
A Benchmark of genetic variant calling pipelines using metagenomic short-read sequencing
10.3389/fgene.2021.648229 · 2021 · External reference
A comprehensive benchmarking of WGS-based deletion structural variant callers
10.1093/bib/bbac221 · 2022 · External reference
A synthetic-diploid benchmark for accurate variant-calling evaluation
10.1038/s41592-018-0054-7 · 2018 · External reference
Best practices for benchmarking germline small-variant calls in human genomes
10.1038/s41587-019-0054-x · 2019 · External reference
Improving SNP discovery by base alignment quality
10.1093/bioinformatics/btr076 · 2011 · External reference
Unresolved reference
2024 · External reference
Tackling the emerging threat of antifungal resistance to human health
10.1038/s41579-022-00720-1 · 2022 · External reference
Bacterial DNA Methylation: a Cell Cycle Regulator?
10.1128/jb.181.17.5135-5139.1999 · 1999 · External reference
Low frequencies of resistance among Staphylococcus and Enterococcus species to the bactericidal DNA polymerase inhibitor N(3)-hydroxybutyl 6-(3’-ethyl-4’-methylanilino) uracil
10.1128/aac.46.12.3770-3775.2002 · 2002 · External reference
Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance
10.1038/ncomms11128 · 2016 · External reference
Molecular evolution of antifungal drug resistance
10.1146/annurev-micro-030117-020345 · 2017 · External reference
Dynamic ploidy changes drive fluconazole resistance in human cryptococcal meningitis
10.1172/jci124516 · 2019 · External reference
Genomic Diversity across Candida auris Clinical Isolates Shapes Rapid Development of Antifungal Resistance In Vitro and In Vivo
10.1128/mbio.00842-22 · 2022 · External reference
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era
10.1093/bib/bbaa101 · 2021 · External reference
SARS-CoV-2 whole-genome sequencing using oxford nanopore technology for variant monitoring in wastewaters
10.3389/fmicb.2022.889811 · 2022 · External reference
Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology
10.1038/s41598-022-16048-y · 2022 · External reference
Nanopore sequencing as a rapidly deployable ebola outbreak tool
10.3201/eid2202.151796 · 2016 · External reference
Minimum error correction-based haplotype assembly: Considerations for long read data
10.1371/journal.pone.0234470 · 2020 · External reference
CLAE: A High-Fidelity nanopore sequencing strategy for read-level viral variant detection and environmental RNA virus discovery
2025 · External reference
Sequencing DNA with nanopores: troubles and biases
10.1371/journal.pone.0257521 · 2021 · External reference
Adjust quality scores from alignment and improve sequencing accuracy
10.1093/nar/gkh850 · 2004 · External reference
Nanopore quality score resolution can be reduced with little effect on downstream analysis
10.1093/bioadv/vbac054 · 2022 · External reference
