I want to create an MSA and then collapse the identical reads, so that I can see the different TYPES of reads in my MSA. Any ideas what program allows such options?
I found a way - I used the fastx program
You don't need to create an MSA in order to achieve this. Dedupe in BBmap does exactly what you want.
This seems close to what I need - but I also need to be able to count the no. of duplicates per type and I can't seem to find this option in the manual...
The endpoint is to count the number of each as per the total reads available.
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