DNA sequence clustering tools
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7.8 years ago
grayapply2009 ▴ 280

Hi guys, I have about 300,000 sequences stored in a fasta file. I am trying to reduce the redundancy of these sequences. I used CD-HIT-EST to remove the redundancy at 95% similarity threshold and am planning to further remove the redundancy with other tools. I tried tgicl but it seems to be a very old and buggy tool, which didn't work well on my fasta file. I am wondering if there are other DNA clustering tools that serve this purpose. Any recommendations?

clustering cdhit redundancy tgicl • 3.6k views
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What was wrong with using CDHIT? Why not try other tools in the suite or alter your threshold?

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7.8 years ago

If I understood you properly then you might want to try with VSEARCH for clustering, de-replication. It is an alternative to commercial USEARCH.

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