Collection of Python scripts for parsing/analysis of reduced representation sequencing data (e.g. RAD-seq, nextRAD). While many of the scripts are functional, some still need considerable cleaning up and more thorough testing - and this repository therefore very much represents a work in progress.
These scripts all require Python 3, with some requiring additional packages (BioPython and NumPy - both of which can be easily installed using the Miniconda or Anaconda installers, or PyVCF - which can be installed using e.g. pip install PyVCF). Usage information for each script can be obtained using the -h or --help flag (e.g. python3 name_of_script.py -h, or is also listed in this README.
This documentation is dynamically generated using the listed README_compile.py script, extracting purpose, usage and links to example files from the argparse information of each script.
vcf_remap2genome.py - script to remap VCF from de novo RAD assembly back to a reference genome
pyrad_find_caps_markers.py - search PyRAD output file for diagnostic CAPS loci that can distinguish two groups (or one group and all other samples)
vcf_clone_detect.py - script to facilitate identification of clones in dataset