methy-pipe

Methy-Pipe: An integrated bioinformatics pipeline for whole
genome bisulfite sequencing data analysis

Written by Peiyong Jiang and Kun Sun.

Download package

The current release of Methy-pipe is version 2.02.
Download the pre-built packages for Linux x86_64 platform: Note that Perl (version 5.8 or higher) and R (version 2.10 or higher) are required.
for R, the package ggplot2 and gridExtra are also required.
If you want pre-built packages for other platforms, please contact the authors.

Manual

Click here to see the manual (PDF).

Testing dataset

We supply the following two testing datasets:
After downloading, please uncompress to the same directory as your Methy-Pipe package and then you can run Methy-Pipe
on these two datasets including read alignment, methylation call and DMR detection (Full dataset only).

For downstream data visualization, we highly recommand BSviewer: a lightweight nucleotide-level, genotyping-preserving
bisulfite sequencing data visualizer that works seamlessly with Methy-Pipe alignments. Find it out now!

Citation

When referencing, please cite "Jiang P, Sun K, Lun FMF, Guo AM, Wang H, et al. (2014) Methy-Pipe: An Integrated Bioinformatics Pipeline
for Whole Genome Bisulfite Sequencing Data Analysis. PLoS ONE 9(6): e100360. doi:10.1371/journal.pone.0100360"   PubMed   Full Paper

Contact

For more inquiries, please contact the authors.


Last update: Jun 25, 2014