jpuritz / dDocent

a bash pipeline for RAD sequencing

RADSeq Bioinformatics and Beyond

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.

Installing

with conda (recommended)

> 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?

Citing dDocent

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

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The "d" is silent 🤫