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hepcat72 / CFF

Cluster-free Filtering. Determine which sequences are real in a metagenomic sample.
GNU General Public License v3.0
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plans to adapt for vsearch? #5

Open gregcaporaso opened 9 years ago

gregcaporaso commented 9 years ago

Hi, I was wondering if you'd thought at all about adapting CFF to use vsearch under-the-hood in place of usearch, since vsearch is open source, has more permissive licensing, etc.

hepcat72 commented 9 years ago

Hi Greg,

Thanks. This has been recently suggested and it sounds like a good idea. Currently, CFF is in a maintenance phase, so we don't have any plans for new features in the immediate future. However if what I've heard is true, and the interface is the same (haven't heard about output format) then it might be worth a try to simply supply vsearch as the usearch executable using the -y option and see what happens. The two scripts which use usearch (and have those options) are getReals.pl & interestingPairs.pl. If you try it out, please let me know how it goes. All this might require is a change to the documentation.

Rob

Robert William Leach 133A Carl C. Icahn Lab Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton, NJ 08544

On Aug 25, 2015, at 5:59 PM, Greg Caporaso notifications@github.com wrote:

Hi, I was wondering if you'd thought at all about adapting CFF to use vsearch under-the-hood in place of usearch, since vsearch is open source, has more permissive licensing, etc.

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