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Old 12-10-2019, 04:32 AM   #2
Senior Member
Location: Switzerland

Join Date: Aug 2008
Posts: 124

What I will do is to write my own script to
1) blastn the sequences against itself (hopefully your sequences are long enough to justify using blast)
2) filter the results to remove blastn results of the same sequences and min e-value
3) Do single linkage clustering based on the blastn results
4) Choose the longest sequence for each cluster

There should be an easier way by using k-mer?!
Melissa is offline   Reply With Quote