Xun Chen (xunchen85)

xunchen85

Geek Repo

Company:Kyoto University

Location:Kyoto

Home Page:https://ashbi.kyoto-u.ac.jp/members/xun-chen/

Twitter:@xunchen85

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Xun Chen's repositories

VIcaller

A software to detect virome-wide integrations

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.

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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

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Bioinformatics_scripts

Useful scripts for various purpose

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VRscreen

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

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