params_illumina.json

{
    "input": "2024.09.24_ROV.csv",
    "spades_mode": "rnaviral",
    "platform": "illumina",
    "agens": "ROV",
    "outdir": "ROV_2024",
    "strategy": "mapping",
    "mapper": "bowtie2",
    "kraken_all": "true",
    "kraken_all_db": "data/kraken_db/db_rotavirus",
    "kraken_focused": "data/kraken_db/db_rotavirus/",
    "save_output_fastqs": "true",
    "save_reads_assignment": "true",
    "references": "data/blast_db/Rotavirus_genomes_ncbi_namesedited.fasta"
}