SummonChimera infers integrated viral genomes with nucleotide precision from NGS data

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

(2013) Jing-Woei Li et al.   BIOINFORMATICS

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

(2013) K. Akagi et al.   GENOME RESEARCH

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

(2013) J. D. Khoury et al.   JOURNAL OF VIROLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Multiplex Identification of Human Papillomavirus 16 DNA Integration Sites in Cervical Carcinomas

(2013) Bo Xu et al.   PLoS One

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

The landscape of viral expression and host gene fusion and adaptation in human cancer

(2013) Ka-Wei Tang et al.   Nature Communications

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

(2012) Yunxin Chen et al.   BIOINFORMATICS

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

(2012) Wing-Kin Sung et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

(2012) Dong Ding et al.   PLoS Genetics

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS