Hi, I am wondering if anyone has used short read data to make MLST profiles. I imagine it would be more time-efficient and maybe even more accurate to map instead of making a de novo assembly. I've only seen a few hints at it in a blog post from Pathogenomics. These include using ICORN and SRST. I think that the other methods on the post use de novo assembly, which I am trying to avoid. ICORN seems like it could be rather involved, but I'm not sure yet, and SRST reportedly doesn't work with newer versions of Samtools.
So has anyone actually hammered out a set of scripts to map reads against an MLST database and determine a profile?
One difficulty that I can imagine is getting the right sequence on the ends of each MLST fragment. Maybe there are more difficulties.