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1. Randomised-proportion Randomised-proportion Public

   Take a fasta file created using window co-ordinates from GLUE and select above a certain proportion then randomly select up to 100 of these

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2. Contamination-Phylogeny Contamination-Phylogeny Public

   Uses phylogeny to identify and remove cross-contamination from a directory containing .sam files using user-specified thresholds

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3. Contamination-Filter Contamination-Filter Public

   Identifies identical reads present in sam files mapped against the same reference genome using a tab delimited file of accession numbers and virus names

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4. AFI AFI Public

   Alignment files from AFI study