AllRice

Code for rice genome analyses (but not necessarily only rice)

Quick Start

The simplest way to get going is to use the AllRice Singularity container available from our Singularity Hub site; e.g.:

cd
git clone https://github.com/BrendelGroup/AllRice
cd AllRice
wget https://BrendelGroup.org/SingularityHub/AllRice.sif
alias rws="singularity exec -e -B ~/AllRice/prj/LHRWBY2021  ~/AllRice/AllRice.sif"
rws ngsutilsj help
rws umi_tools --help
rws flye --help
wget https://BrendelGroup.org/SingularityHub/DDN.sif
singularity exec -e -B ~/AllRice/prj/LHRWBY2021  ~/AllRice/DDN.sif  DiscovarDeNovo -h

In the above example, you clone this repository into your Linux home directory, go into the thus created AllRice directory, download the AllRice Singularity container, define the bash alias rws ("run with singularity"), and check that everything works by showing help information on some of the installed programs. You then also download the DDN.sif image and show that you have the DiscoverDeNovo assembler accessible. For a listing of included software, see our CATALOG.

Of course this assumes that you have Apptainer/Singularity installed on your system. Check whether there is package built for your system. Otherwise, follow the instructions to install Singularity from source code.

Projects

• LHRWBY2021 Computational analyses discussed in

Luo, D., Huguet-Tapia, J.C., Raborn, R.T., White, F.F., Brendel, V.P. & Yang, B. (2021) The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. Plant Communications 2, 100164.

Follow the instructions in 0README to reproduce the work (or use the workflow as a template for analysis of your own data sets).

Contact

Please direct all comments and suggestions to Volker Brendel at Indiana University.