SnpHub is a Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.
For more details, check our tutorial
For Docker-encapsulated version, check here
To start a general setup, see here
Here are our live demos.
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
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
- crayon
- ggmap
- dplyr
- rjson
- shiny
- pegas
- maps
- vcfR
- ape
- DT
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 yourshiny-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.
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