Bisulfite Aligners

  • BS Seeker
  • Website Github

    BS Seeker performs accurate and fast mapping of bisulfite-treated short reads. It aligns Bisulfite-treated reads generated from the Cokus et al's library protocol (with tags) or the Lister et al's library protocol (with no tags).

    BS Seeker 可用於比對亞硫酸鹽處理過後的短DNA片段,它可以同時分析比對早期有標記的樣本庫(Cokus等人所建)與 目前一般常用 BS-seq 的無標記樣本庫(Lister等人建)的亞硫酸鹽處理後的DNA片段。

  • BS Seeker2
  • Website Github

    BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.

    BS Seeker2 是一個新一代準確且快速地分析比對亞硫酸鹽處理後之DNA短片段的工具。此版本被廣泛使用在大量全基因體DNA甲基化定序論文。

  • BS Seeker3
  • Github Dockerhub

    BS-Seeker3 maps bisulfite-treated reads (bs-seq) with high accuracy and ultra-fast speed.

    BS Seeker3 為一個超高速地分析比對亞硫酸鹽處理後之DNA短片段的工具。

Methylome Analyzers

  • MethGo
  • Website Github

    MethGo is designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).

    MethGo 是一個用於分析來自全基因組甲基化亞硫酸鹽定序資料的工具。

  • TEA
  • Website

    Analyzing and visualizing data from whole-genome BS-Seq (WGBS) experiments conducted in the model plant Arabidopsis thaliana.

    TEA 為模式植物阿拉伯芥的全基因組亞硫酸鹽定序實驗的分析及視覺化工具。

  • EpiMOLAS
  • Website Dockerhub

    An intuitive web-based framework for genome-wide DNA methylation analysis.

    EpiMOLAS 是用於分析全基因組DNA甲基化的生物資訊工具。

  • MethGet
  • Website Github

    A web-based bioinformatics software for correlating DNA methylation and gene expression.

    MethGet 是一個分析全基因組DNA甲基化和基因表現間相關性的網站。

  • MethylC-analyzer
  • Github Dockerhub

    MethylC-analyzer is specifically for analyzing and visualizing post-alignment of WGBS and RRBS on both CG and non-CG sites.

    MethylC-analyzer 是專門用於WGBS和RRBS序列比對後的CG和非CG位點上的分析和視覺化工具。

  • BSImp
  • Github

    BSImp is a probabilistic-based imputation that uses information from neighbouring sites to recover partially observed methylation patterns speedily.


  • MeH
  • Github

    MeHscr is a tool for estimating methylation heterogeneity in bisulfite sequencing data by mathematical modelling.


Chromatin Accessibility and Histone Modifications

  • ATACgraph
  • Github Dockerhub

    A bioinformatics tool for ATAC-seq specific QC, data analysis, and visualization.

    ATACgraph 是一個專門分析及視覺化 ATAC-seq 的分析工具。用於尋找染色質開放區域及基因。

  • QHistone
  • Website

    A web-based query database for predicting the epigenome profile query, and studying syngergistic/antagonistic effect for Arabidopsis.

    QHistone 是一個預測模式植物阿拉伯芥表觀基因組圖譜與蛋白之間交互作用的資料庫。

Fungal Genomics

  • FunCore