My project is mainly focusing on analyzing Restriction-site associated DNA sequencing (RAD-seq), I will keep updating the methods of how to deal with RAD data and how to do population genomes and phylogenomics analyze on RAD-seq data.
1. Software install
Since the sequencing data is usually gigantic, you want to analyze them on HPC. So please contact your IT whether the software has already been installed.
2. Environmental setup in an HPC cluster
If you want to install some latest compilers, software, and packages in your local directory without root permission, you can follow this instruction by Yi-Jyun Luo from Marine Genome Unit of OIST.
3. Stacks pipeline