ggavelis/HGT_v_Contamination_assessor

How can we discriminate contaminants from HGT? Alien indices are often used to screen out foreign sequences, but can 'overclean' by removing bona fide HGT. This script leverages metadata about each DNA/AA sequence (i.e. whether it is spliced, has a polyA tail or spliced leader), and uses that to assess the extent to which AI-based cleaning is removing legitimate HGT.

Python