DNA sequence clustering tools · Biostar

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DNA sequence clustering tools

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

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updated 9.3 years ago by Biostar

• written 10.2 years ago by ngs101.com

What was wrong with using CDHIT? Why not try other tools in the suite or alter your threshold?

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written 9.3 years ago by Joe

1 answer

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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written 10.2 years ago by Bioinformatics_NewComer

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