VODKA --genomeFA <input fasta> --queryInput <file of fastq/fasta> --outDir <output directory> \
--bt2Dir <bowtie2 directory> --webLogo <webLogo> [options]
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--genomeFA <input fasta> : viral genome fasta file.
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--queryInput <fastq/fastq> : a file with full path of fastq or fasta files for alignment. fastq/fasta files can be gzip'ed.
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--outDir <output directory> : full path to output directory.
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--bt2Dir <bowtie2 directory> : full path to bowtie2-2.2.9 directory. (where bowtie2 and bowtie2-build is located)
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--webLogo <webLogo> : full path to webLogo.
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options :
- -bp_from_right <n> : <n> is number of bases from right. (default: 3000)
- -h/--help : print this usage.