Kmer analysis of large amino acid datasets
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Entering edit mode
10 months ago
eeveeody • 0

Hi There! I have a large file of amino acid sequences. I've been using the kcount function from the kmer R package as a part of my workflow. Unfortunately, as my datasets have grown this is starting to take a super long time. I'd like to find something like Jellyfish that will allow me to tackle this problem in parallel. Unfortunately, Jellyfish can't be used for AA. I'm going to try this mercat package ( https://github.com/pnnl/mercat ), but I've noticed there aren't any posts about it here. Just wondering if anyone has used it or if there's something better I don't know about. I found this related post from ~3 years ago, but it's not a perfect fit for my issue(Can we use JELLYFISH for amino acid seqeunces? ). Thanks and happy holidays!

sequencing kmer • 333 views
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