mothur

ICoMM working group

I spent this week in Bremen, Germany helping the folks with the International Census of Marine Microbes think about how to analyze the more than 8 million V6 sequence reads they have generated for various projects over the past several years. It was an all star cast with appearances from Chris Quince (pyronoise), Rob Knight (unifrac), John Bunge (parametric estimation of richness), Mitch Sogin (pyrosequencing pioneer), Jim Cole (RDP), Frank Oliver Glockner (SILVA), and a number of other marine microbial ecologists. I’m not sure if ICoMM got anything out of our three days of rambling, but here’s what I took away…

    1. I need to check out PyroNoise because it really seems to have an amazing impact on noise filtering from 16S data
  1. We need to incorporate John and Chris’s tools for fitting species-abundance data to parametric models into mothur
  2. Jet lag sucks

John’s tool (catchall) is very useful, and it would be wonderful to see it incorporated into mothur. In fact, he and I have talked about that. I honestly think it wouldn’t be too hard to fold in his command line version.

Here is the link to his stuff (for anyone who’s interested):
http://catchall.cac.cornell.edu/

I am running my 454 dataset through PyroNoise right now… it does have a huge impact on the diversity of sequences in the dataset, but is not very user-friendly! Plus it is very computationally expensive; my computer ran for three weeks straight to push data from a single 454 run through PyroNoise.

If anyone wants to try it on a Mac, I did get it working on my MacBook Pro. It took a few changes, reported here: http://seqanswers.com/forums/showthread.php?t=3588

awesome, thanks! i’ll give it a try this morning.