fastq as input data

[carlottaolivero]

Does Scorpio work with fastq as input data? Can you select a minimum frequency threshold for mutations in order for scorpion to select a variant? this is for samples containing mixed variant. thanks

[rmcolq]

Currently scorpio only works with aligned fasta and assumes that each fasta entry is a consensus genome. We do not plan to allow it to process raw reads. We are working on adding a feature that might allow a user to spot contamination from a mixture (resulting in a mixture of constellations) or even recombination, but I don't think this would apply to your use case