Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

(2018) Norman Goodacre et al.   mSphere

Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies

(2018) Sébastien Massart et al.   PHYTOPATHOLOGY

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection

(2017) Arifa S. Khan et al.   mSphere

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Towards next-generation sequencing analytics for foodborne RNA viruses: Examining the effect of RNA input quantity and viral RNA purity

(2016) Zhihui Yang et al.   JOURNAL OF VIROLOGICAL METHODS

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

(2016) Edward T. Mee et al.   VACCINE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Sequencing of long stretches of repetitive DNA

(2016) Alfredo De Bustos et al.   Scientific Reports

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

(2016) Timokratis Karamitros et al.   PLoS One

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

RAMPART: a workflow management system for de novo genome assembly

(2015) Daniel Mapleson et al.   BIOINFORMATICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent

(2015) Linlin Li et al.   JOURNAL OF VIROLOGICAL METHODS

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

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

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

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

(2014) Daniel Langenkämper et al.   BMC BIOINFORMATICS

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Census-based rapid and accurate metagenome taxonomic profiling

(2014) Amirhossein Shamsaddini et al.   BMC GENOMICS

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Identification of a Novel Rhabdovirus in Spodoptera frugiperda Cell Lines

(2014) H. Ma et al.   JOURNAL OF VIROLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

CDD: NCBI's conserved domain database

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

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing

(2014) Shasta D. McClenahan et al.   VACCINE

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

(2014) S. Poux et al.   Database-The Journal of Biological Databases and Curation

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

MetaID: A novel method for identification and quantification of metagenomic samples

(2013) Satish M Srinivasan et al.   BMC GENOMICS

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

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

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads

(2012) Hongmei Jiang et al.   PLoS One

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) Y. Zhao et al.   BIOINFORMATICS

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The International Nucleotide Sequence Database Collaboration

(2011) I. Karsch-Mizrachi et al.   NUCLEIC ACIDS RESEARCH

Next Generation Sequencing Technologies for Insect Virus Discovery

(2011) Sijun Liu et al.   Viruses-Basel

Viral Nucleic Acids in Live-Attenuated Vaccines: Detection of Minority Variants and an Adventitious Virus

(2010) J. G. Victoria et al.   JOURNAL OF VIROLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Unsupervised statistical clustering of environmental shotgun sequences

(2009) Andrey Kislyuk et al.   BMC BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

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

The National Center for Biotechnology Information's Protein Clusters Database

(2008) William Klimke et al.   NUCLEIC ACIDS RESEARCH