Sequencing methods for HA and NA genes of avian influenza viruses from wild bird feces using Oxford Nanopore sequencing

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

(2022) Derek Tshiabuila et al.   BMC GENOMICS

Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences

(2022) Andy R. Vierstraete et al.   Ecology and Evolution

Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing

(2022) Ekaterina Avershina et al.   Frontiers in Microbiology

Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology

(2022) Ellen M. de Vries et al.   Scientific Reports

Nanopore sequencing as a rapid tool for identification and pathotyping of avian influenza A viruses

(2021) Beate M. Crossley et al.   JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units

(2021) Guilherme Marcelino Viana de Siqueira et al.   Frontiers in Public Health

Epidemiologic Survey of Avian Influenza Virus Infection in Shorebirds Captured in Hokkaido, Japan

(2020) Masayoshi Kakogawa et al.   JOURNAL OF WILDLIFE DISEASES

Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2

(2020) Wai Sing Chan et al.   Virology Journal

Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

(2019) Lucas M. Ferreri et al.   Ecology and Evolution

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE

(2019) Chelsea G. Himsworth et al.   JOURNAL OF WILDLIFE DISEASES

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Phylogenetic variations of highly pathogenic H5N6 avian influenza viruses isolated from wild birds in the Izumi plain, Japan, during the 2016-17 winter season

(2018) Makoto Ozawa et al.   Transboundary and Emerging Diseases

Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study

(2018) Kazuo Imai et al.   Frontiers in Microbiology

Characterizing the temporal patterns of avian influenza virus introduction into Japan by migratory birds

(2017) Manabu ONUMA et al.   JOURNAL OF VETERINARY MEDICAL SCIENCE

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Genetic diversity of highly pathogenic H5N8 avian influenza viruses at a single overwintering site of migratory birds in Japan, 2014/15

(2015) M Ozawa et al.   Eurosurveillance

Detection of highly pathogenic zoonotic influenza virus H5N6 by reverse-transcriptase quantitative polymerase chain reaction

(2015) Hans G Heine et al.   Virology Journal

A Complete Molecular Diagnostic Procedure for Applications in Surveillance and Subtyping of Avian Influenza Virus

(2014) Chun-Hsien Tseng et al.   Biomed Research International

Universal Primer Set for Amplification and Sequencing of HA0 Cleavage Sites of All Influenza A Viruses

(2008) A. Gall et al.   JOURNAL OF CLINICAL MICROBIOLOGY