Example_configuration.txt

##########################################
    ## Input data can be: (a) an alignment file (in BAM format); or (b) FASTQ file(s) (preferred) – for
    ## single end data, “fastq1” is required; for paired-end, both “fastq1” and “fastq2” are needed.
    ##########################################
    # alignment_file = /scratch/kingw/virusFinder/simulation/simulation..bam
    fastq1 = test1
    fastq2 = test2
    detect_integration = yes
    detect_mutation = no
    mailto = 
    thread_no = 8

    ##########################################
    ## The full paths to the following third-party tools are required by VirusFinder:
    ##########################################
    blastn_bin = /usr/local/src/ncbi-blast-2.2.26+/bin/blastn
    bowtie_bin = /usr/local/bin/bowtie2
    bwa_bin = /usr/local/bin/bwa
    trinity_script = /usr/local/src/trinityrnaseq_r2012-06-08/Trinity.pl
    SVDetect_dir = /usr/local/scr/SVDetect_r0.8

    ##########################################
    ## Reference files (indexed for Bowtie2 and BLAST)
    ##########################################
    virus_database = /Users/mbrown/GitHub/VirusIdentification/VirusFinder2/VirusFinder2_VERSE/./virus_reference/virus.fa
    bowtie_index_human = /Users/mbrown/GitHub/VirusIdentification/VirusFinder2/VirusFinder2_VERSE/human_reference/GRCh38.genome
    blastn_index_human = /Users/mbrown/GitHub/VirusIdentification/VirusFinder2/VirusFinder2_VERSE/human_reference/GRCh38.genome
    blastn_index_virus = /Users/mbrown/GitHub/VirusIdentification/VirusFinder2/VirusFinder2_VERSE/./virus_reference/virus

    ##########################################
    ## Parameters of virus insertion detection (VERSE algorithm). They are ignored for single-end data
    ##########################################
    detection_mode = normal
    #If not specified, VirusFinder runs in normal detection mode.
    flank_region_size = 4000
    #normal, it (and ‘sensitivity_level’ below) will be ignored.
    sensitivity_level = 1
    #sensitivity, and accordingly more computation time.

    ##########################################
    ## Parameters of virus detection. Smaller “min_contig_length”, higher sensitivity
    ##########################################
    min_contig_length = 300
    blastn_evalue_thrd = 0.05
    similarity_thrd = 0.8
    chop_read_length = 25
    minIdentity = 80