18 Pathogen Reference Fasta including indexes
18 pathogens were downloaded using ncbi datasets to downloaded the refseq reference genomes for the following viruses and single eukaryotic parasite Toxo gondii.
in_genome=("Herpes Simplex Virus 1" "Herpes Simplex Virus 2" "Varicella Zoster Virus" "Epstein-Barr Virus" "Human Cytomegalovirus" "Human Herpesvirus 6A" "Human Herpesvirus 6B" "Human Herpesvirus 7" "Human gammaherpesvirus 8" "Hepatitis B Virus" "Hepatitis C Virus" "Human T-lymphotropic Virus 1" "Human Immunodeficiency Virus 1" "Human Polyomavirus BKV" "Human Polyomavirus JCV" "Merkel Cell Polyomavirus" ) pro_genome=( "Toxoplasma gondii" "Chlamydia trachomatis" "Helicobacter pylori" )
After doing benchmarking on a subset of samples it became clear that one contig NW_017384310.1 had 100% positivity across all tested samples.
In fact this has been previously discussed https://www.nature.com/articles/s41431-019-0494-2.
Thus, the standard refseq genome has serious missassembly issues.
This motivated to use a more recently assembled reference sequence which as made using long read technologies + Hi-C. GCA_019455545.1
Added this reference onto the viral sequences and indexed with bowtie2.