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ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.

VIcaller

A software to detect virome-wide integrations

VariabilityInTEs

RFAPtools

We developed a bioinformatics pipeline termed RFAPtools to unambiguously discriminate between SNPs versus differences of homoeologous sequences in polyploid crops such as oilseed rape without a reference genome sequence

TE-MPRA-and-phylogenetic-analysis

VRscreen

This pipeline can be used to detect uniquely mapped paired-end viral reads

Bioinformatics_scripts

Useful scripts for various purpose

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