MSA program that allows collpase of identical reads

Question

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Hi,

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?

Thanks,

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I found a way - I used the fastx program http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_collapser_usage

Answer 1

[Mensur Dlakic]

You don't need to create an MSA in order to achieve this. Dedupe in BBmap does exactly what you want.

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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.