dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set. It is designed to run on Linux based machines with large memory capacity and multiple processing cores, and it can be modified for use on HPC.
> conda install -c bioconda ddocent # or into a fresh environment # > conda create -n environmentname -c bioconda ddocent
If you are getting samtools errors:
> conda install -c bioconda ddocent 'samtools>=1.10' # or into a fresh environment # > conda create -n environmentname -c bioconda ddocent 'samtools>=1.10'
Alternatively, it's recommended to use mamba as your conda solver.
manually (no longer directly supported)
> git clone https://github.com/jpuritz/dDocent.git > cd dDocent > chmod +x ./install_dDocent_requirements > sh ./install_dDocent_requirements
How does dDocent compare?
Puritz JB, Hollenbeck CM, Gold JR. 2014. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ 2:e431 https://doi.org/10.7717/peerj.431
The "d" is silent