Identification of novel ERV integrations in WGS data
Mason AS, Lund AR, Hocking PM, Fulton JE & Burt DW (2020), Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data, Mobile DNA, 11:22.
Moved repo from old github account (andrewstephenmason) to here (asmasonomics).
The s6-v2_extract_putative_sites.py script is a replacement for the S6 script. However, this is only skeleton code at this stage, as it has not been adapted for use in other systems (dependencies etc.)
The package was developed to help with ALVE annotation and validation as the numbers expanded outside the original use of obsERVer in commercial layers.
The repo replaces "ALVE_ID_pipeline" which was referenced in my thesis. These scripts have been maintained in the _replaced_ALVE_ID_pipeline/ directory.