This repository contains code used in the development of the FecalSeq method for enriching host DNA from feces, by Kenneth Chiou (website) and Christina Bergey (website). A paper describing the method been submitted for publication and is available as a preprint from bioRxiv.
The most up to date accompanying labwork protocol can be found in this repository.
- Mapping and variant identification uses the commands
from
fecalRAD_analysis_cmds_through_variant_ID.shand makes use of the mapping pipeline from the repo, NGS-map. - Subsequent analytical steps are summarized in
RADfaex_cmds.sh.