Clustering long-read 18S amplicons about identity HOT 3 OPEN

and now starting run 6...

from identity.

Hi, Pierre.

Thanks for your interest in MeShClust v3.0.

No, you are not doing any thing wrong. MeShClust v3 should take longer than MeShClust v1 because of the all-vs-all done at the beginning and when there are enough sequences are accumulated in the reservoir.

The current version does NOT log the results (this is a good feature to include in the next release God willing).

The -p parameter controls the number of data passes (default: 10). The algorithm may converge before the 10th iteration if the number of clusters does not change during a data pass. The good news is that the algorithm should run faster in late iterations than the early ones because it may not need to do as many as of the all-vs-all blocks.

If you would like to speed up the algorithm in the future, you may want to reduce the size of the all-vs-all block (-b) and increase the size of the batch (-v).

Please keep me posted.

Hani Z. Girgis, PhD

from identity.

Hello again, Pierre.

I am working on the next version of MeShClust. It would be very helpful to use your data while developing and testing it. Are the 16S or the 18S data already published? If yes, where can I download the data set(s). Feel free to email me at hzgirgis at buffalo dot edu.

Best regards.

Hani Z. Girgis, PhD

from identity.