HGT analysis pipeline

pseudo_code

import annotated genomes

for genome in genomes:
  write genome to genome_database
    database{
            species_name:
              CDS{
                  annotation:
                  aa sequence:
                  nt sequence:
                  3' position:
                  5' position:
                  }
            }

for CDS in species_database:
  BLAST against all other species
  if hit > 99% identical
    write to HGT_database:
      query_CDS{
              hit_CDS1:
              hit_CDS2:
              ... etc
              }

for hit in HGT_database:
  if 3' or 5' within ~100bp of other_hit:
    add hit and other_hit to group
    align hits and deduplicate

for CDS in groups:
  get annotations