We assume your current directory points to this directory (data)
Download and process each dataset so that they are fully ready to be used in the evaluation step:
bash download_d1_sars-cov-2_r94.sh #Download Dataset D1 SARS-CoV-2
bash download_d2_ecoli_r94.sh #Download Dataset D2 E. coli
bash download_d3_yeast.sh #Download Dataset D3 Yeast
bash download_d4_green_algae.sh #Downlaod Dataset D4 Green Algae
bash download_d5_human_na12878.sh #Download Dataset D5 Human HG001
#Prepare the contamination dataset
cd contamination && bash generate_fast5_files.sh && cd ..
#Prepare the relative abundance dataset
cd relative_abundance && bash generate_fast5_files.sh && bash generate_ref.sh && cd ..
#Create a random community of randomly ordered reads from D1-D5 reads read_ids.txt
cd random_community && bash 0_generate_random_ids.sh && bash 1_symbolic_links.sh && cd ..