Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

(2017) Yi Zheng et al.   VIROLOGY

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses

(2017) Emilyn Matsumura et al.   Viruses-Basel

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

(2017) Sebastien Massart et al.   Frontiers in Microbiology

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data

(2017) Guillaume Carissimo et al.   PLoS One

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

(2016) Yeonhwa Jo et al.   BMC GENOMICS

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Advances in Faba Bean Genetics and Genomics

(2016) Donal M. O'Sullivan et al.   Frontiers in Genetics

VIP: an integrated pipeline for metagenomics of virus identification and discovery

(2016) Yang Li et al.   Scientific Reports

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data

(2015) Yeonhwa Jo et al.   Scientific Reports

A Top Ten list for economically important plant viruses

(2014) Edward P. Rybicki   ARCHIVES OF VIROLOGY

KAnalyze: a fast versatile pipelined K-mer toolkit

(2014) Peter Audano et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

(2014) Bo Liu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Comprehensive Human Virus Screening Using High-Throughput Sequencing with a User-Friendly Representation of Bioinformatics Analysis: a Pilot Study

(2014) Tom J. Petty et al.   JOURNAL OF CLINICAL MICROBIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics on the Cloud Computing Platform Azure

(2014) Hugh P. Shanahan et al.   PLoS One

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

(2014) Stephen J. Wylie et al.   PLoS One

Development of a virus detection and discovery pipeline using next generation sequencing

(2014) Thien Ho et al.   VIROLOGY

Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana : analysis of distribution and functions

(2013) Sony Malhotra et al.   NUCLEIC ACIDS RESEARCH

The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome

(2013) C. Da Silva et al.   PLANT CELL

VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data

(2013) Qingguo Wang et al.   PLoS One

Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

(2013) Guoyan Zhao et al.   PLoS One

Methods in virus diagnostics: From ELISA to next generation sequencing

(2013) Neil Boonham et al.   VIRUS RESEARCH

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

CloudMan as a platform for tool, data, and analysis distribution

(2012) Enis Afgan et al.   BMC BIOINFORMATICS

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

(2012) R. Burke Squires et al.   Influenza and Other Respiratory Viruses

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

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs

(2012) M. Kashif et al.   PLANT DISEASE

Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation

(2012) Rugang Li et al.   PLoS One

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Facilitative and antagonistic interactions between plant viruses in mixed infections

(2011) JERZY SYLLER   MOLECULAR PLANT PATHOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

ViPR: an open bioinformatics database and analysis resource for virology research

(2011) Brett E. Pickett et al.   NUCLEIC ACIDS RESEARCH

Sweetpotato Viruses: 15 Years of Progress on Understanding and Managing Complex Diseases

(2011) Christopher A. Clark et al.   PLANT DISEASE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

(2010) Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

(2010) Beatrix Coetzee et al.   VIROLOGY

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH