New version of EMIRGE posted to github, and other news

[Chris Miller]

I.  I've just posted an updated version of EMIRGE to github.  This version now works with the newly released usearch v6.  It is not backwards compatible with earlier versions of usearch, as the command line and some functionality has changed substantially.  Please let me know how this new version works for you.

II.  As of about a month ago, there are now two versions of EMIRGE.  

1. emirge.py -- the standard version of EMIRGE designed to work with metagenomic data
2. emirge_amplicon.py -- this version should be able to handle large numbers of reads (up to a few million) that are all generated from a gene of interest (e.g. the 16S rRNA gene).  This could also be used for transcriptome data, in theory.  There are several space for speed tradeoffs, much more efficient code, etc.  This version currently loads all reads in memory, which places a limit on how much can be processed.
   

Eventually, the two code bases will be merged.  The second script (emirge_amplicon.py) was employed in a submitted manuscript describing the use of EMIRGE on amplicon data.

III.  I and EMIRGE development are moving to the University of Colorado Denver.  If you are interested in EMIRGE or more generally in systems-level approaches to studying microbial communities and/or bioinformatics, and looking for a place to work in a lab, attend graduate school (Masters or PhD), or do postdoctoral research, please contact me.

  

Thanks,

Chris