Use de novo scaffold blast to determine how many, and which, strains are in the sample

[jonbra]

Description of feature

What should be the critera? I guess if there are more than one scaffold that gives a decent blast hit that is different from the best one? E.g., if there is only one scaffold present, then choose the top blast hit as the reference. If there are two or more scaffolds and they all give the same reference, or the same genotype, as blast hit then there is only one strain present. If there are two or more scaffolds and they give different genotypes as blast hits, and both hits are good, then there are two strains presen.t

[jonbra]

See also the rotavirus workflow and the phylogenetic approach