Detection and genotyping of transposable element variants
ERVcaller : Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019. PMID: 30895294
Detection of viral integrations, and power 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
Viral sequence prediction
VirusPredictor : XGBoost-based software to predict virus-related sequences in human data. Bioinformatics. 2024. PMID: 38597887.
Other genomic databases or resources
ViralReferences : A in-house database of viral reference sequences in FASTA format. Genomics. Genomics. 2021 PMID: 33301893
BatchEffect : Scripts to identify batch effects (sequencing facility-/DNA
source-associated reads) in deep sequencing data. Genomics. 2021 PMID: 33301893
GACT : A Genome
build and Allele
definition Conversion
Tool
for SNP imputation and meta-analysis in genetic association studies. BMC Genomics. 2014 |