snphub

SnpHub is a Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.

Our homepage

For more details, check our tutorial

For Docker-encapsulated version, check here

To start a general setup, see here

Here are our live demos.

Citation

Please cite SnpHub as follow:

Wenxi Wang, Zihao Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Mingming Xin, Huiru Peng, Yingyin Yao, Qixin Sun, Weilong Guo, SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat, GigaScience, Volume 9, Issue 6, June 2020, giaa060, https://doi.org/10.1093/gigascience/giaa060

Environment request

To run the SnpHub, make sure the following software programs are already installed:

samtools (≥ v1.4)
bcftools (≥ v1.8)
seqkit
tabix (≥ v1.6)

Also, the following R packages are also prerequisites:

ggplot2 (v3.3.2)
crayon
ggmap
dplyr
rjson
shiny
pegas (v0.11)
maps
vcfR
ape
DT

Demo

Two steps are needed to run on demo data set:

Using git to clone SnpHub to local.

git clone https://github.com/esctrionsit/snphub

Using R to run on demo data set. (Or copy the SnpHub into your shiny-server app folder)

R -e "shiny::runApp('./snphub', port=5000, host='0.0.0.0')"

Make sure that samtools, bcftools, seqkit and tabix are added to system PATH. Otherwise, tool application paths part in setup.conf is needed to change to fit.

Setup on own data set

Fulfill config file

Basic config file is named setup.conf, fulfill it and then run command:

Rscript ./setup.R

Check configuration for more details about setup.conf.

Check file format for more details about required file formats.

If it is your first time to set up SnpHub, you need to delete advanced_config.R, and then rename advanced_config_O.R to advanced_config.R.

For more details, check our tutorial