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Detection and genotyping of endogenous retrovirus (ERV) insertions

ERVcaller :  Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019. PMID: 30895294



Clonal viral integration analysis

VIcaller : A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Research. 2019. PMID: 30872350

VIpower : Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing. Genomics. 2020. PMID: 30710609

UvirusPredict : A tool to predict the presence of uncharacterized viral sequences in human sequence data. (Under review)



Others

ViralReferences
: A in-house database of viral reference sequences in FASTA format. Genomics. 2020. Under review

BatchEffect : Scripts to identify batch effects (sequencing facility- or DNA sources-associated reads) in high-throughput sequencing data. Genomics. 2020. Under review

GACT : A Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies. BMC Genomics. 2014