mothur v.1.23.0
We are happy to release our first offering of 2012 - mothur_v.1.23.0. This promises to be yet another exciting year for developing and supporting mothur!
The current release has a number of useful new commands and important feature updates that you will certainly want to check out. You may be interested in checking out two of the new commands. First, we have added yet another chimera detection approach - Persues - as chimera.perseus. Our testing suggests that it is about as good as chimera.uchime. Second, we also added shhh.seqs which is a sequence denoising algorithm originally developed by Chris Quince. We don’t like it as well as pre.cluster, but feel free to play with it an form your own opinion. On the options front, we have continued to add parallelization to a number of commands for Windows users. We have also added q-values to the output from metastats so that the output is more in line with the original R code. Finally, we have updated the Schloss SOP, which reflects how my lab uses mothur to process sff files and was published recently in PLoS ONE and we have posted a mothur-compatible version of a greengenes-formatted taxonomy training set that contains >80k sequences.
As always, we appreciate your feedback, recommendations, and questions. We are planning on hosting another workshop in the Detroit area this April 23-25. If you are interested in attending, please email pdschloss\@gmail.com to reserve your seat.
Keep the citations coming...
Pat Schloss
New commands
- chimera.perseus - a mothur-based rewrite of Chris Quince’s chimera detection program, Perseus
- shhh.seqs - a mothur-based rewrite of Chris Quince’s sequence denoting program, SeqNoise
- summary.qual - summarize the contents of quality score files
Feature updates
- metastats - added values
- pre.cluster - added processors option for Windows (option now available for all operating systems)
- chimera.uchime - added processors option for Windows (option now available for all operating systems)
- chimera.slayer - added processors option for Windows (option now available for all operating systems)
- get.oturep - fasta parameter is no longer required
- chimera.uchime - added column headings to output
- screen.seqs - added taxonomy parameter
- heatmap.sim and venn - added fontsize parameter
- sens.spec - fixed label option and added smart distancing.
- pre.cluster - added map output file
- added warning that mothur does not support protein sequences
Bug fixes
- trim.flows - fixed bug that occurred if you had multiple primers with blank names - https://forum.mothur.org/viewtopic.php?f=4&t=1358
- chimera.uchime - executable location - https://forum.mothur.org/viewtopic.php?f=4&t=1379
- classify.seqs - mothur couldn’t handle parentheses in the taxonomy file. - https://forum.mothur.org/viewtopic.php?f=4&t=1370
- chimera.bellerophon - https://forum.mothur.org/viewtopic.php?f=4&t=1151 - segfault in chimera.bellerophon MPI-Enabled version.
- chop.seqs - had an off by one error - if you put numbases=200 the sequence came out as 199 bases
- trim.seqs - fixed flip parameter in - https://forum.mothur.org/viewtopic.php?f=4&t=1401&p=3486#p3486
- fixed bug with newly paralellized commands for Windows that was causing crashes - https://forum.mothur.org/viewtopic.php?f=4&t=1422
- get.groups and remove.groups file mismatch - https://forum.mothur.org/viewtopic.php?f=4&t=1396&p=3560#p3560
Wiki updates
- Added the larger greengenes reference taxonomy that was recently published to the list of greengenes-formatted databases
- 454 SOP - updated documentation to reflect the final version of the recently published PLoS ONE manuscript
Registered users
2046 - 1/9/2012