Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

(2015) Xutao Deng et al.   NUCLEIC ACIDS RESEARCH

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

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

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Detection of novel divergent arenaviruses in boid snakes with inclusion body disease in The Netherlands

(2013) R. Bodewes et al.   JOURNAL OF GENERAL VIROLOGY

Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

(2013) John L. Mokili et al.   PLoS One

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

(2013) Aarti Desai et al.   PLoS One

Comparative analysis of de novo transcriptome assembly

(2013) Kaitlin Clarke et al.   Science China-Life Sciences

Gossamer -- a resource-efficient de novo assembler

(2012) T. Conway et al.   BIOINFORMATICS

A de novo metagenomic assembly program for shotgun DNA reads

(2012) Binbin Lai et al.   BIOINFORMATICS

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

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo)

(2012) A. Boros et al.   JOURNAL OF GENERAL VIROLOGY

A third gyrovirus species in human faeces

(2012) T. G. Phan et al.   JOURNAL OF GENERAL VIROLOGY

Acute Diarrhea in West African Children: Diverse Enteric Viruses and a Novel Parvovirus Genus

(2012) T. G. Phan et al.   JOURNAL OF VIROLOGY

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

(2012) T. F. F. Ng et al.   JOURNAL OF VIROLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

The changing face of pathogen discovery and surveillance

(2012) W. Ian Lipkin   NATURE REVIEWS MICROBIOLOGY

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data

(2012) Xianwen Ren et al.   PLoS One

Discovery of a Novel Polyomavirus in Acute Diarrheal Samples from Children

(2012) Guixia Yu et al.   PLoS One

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

(2012) Gilda Grard et al.   PLoS Pathogens

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Identification of a novel astrovirus in domestic sheep in Hungary

(2011) Gábor Reuter et al.   ARCHIVES OF VIROLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses

(2011) L. Li et al.   JOURNAL OF GENERAL VIROLOGY

The Fecal Viral Flora of California Sea Lions

(2011) L. Li et al.   JOURNAL OF VIROLOGY

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue

(2011) Richard A. Moore et al.   PLoS One

Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results

(2011) Niina Haiminen et al.   PLoS One

A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing

(2011) Gordon M. Daly et al.   PLoS One

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

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

(2008) H. Feng et al.   SCIENCE

Rapid Identification of Known and New RNA Viruses from Animal Tissues

(2008) Joseph G. Victoria et al.   PLoS Pathogens