We have released mothur v.1.32.0 and have a number of exciting new features and updates to tell you about. The main new feature is to incorporate the LEfSe software package from Curtis Huttenhower’s lab into mothur as the lefse command. Alternatively, you could use the make.lefse command to generate a file to use as input to LEfSe. They should produce the same output, let us know if you think we’re missing anything. We also incorporated the Kruskal-Wallis non-parametric test (think ANOVA) as the kruskal.wallis command - this is part of the LEfSe algorithm. Among the new features we’ve renamed a couple of commands (see below) and improved the output generated by the classify.rf command (formerly the classify.shared command. We are putting the finishing touches on classify.svm, which will be similar to classify.rf (random forest), but uses support vector machines (SVMs). As always, there have been a number of bugs reported that we’ve addressed in this release. We also noticed that the greengenes folks expanded their database and taxonomy and we have updated the mothur-compatible versions of those. Going forward we’re looking to add a number of new commands for the next release including a SRA submission tool. If you have any suggestions for other commands or options, let us know!
Finally, there are still seats available for the R workshop in November and the mothur workshop in December. Consider coming to one or both - Detroit is beautiful that time of year.
- rename.seqs - https://forum.mothur.org/viewtopic.php?f=5&t=1918
- make.lefse - creates a lefse compatible input file from mothur’s output files.
- kruskal.wallis - find the Kruskal Wallis one way analysis of variance for each OTU.
- lefse - modelled after the lefse program written by the Huttenhower lab.
- get.metacommunity changed to get.communitytype.
- classify.shared changed to classify.rf
- classify.seqs - removed extra name checks for speed up of reading taxonomy file.
- screen.seqs - allowed for fractional percent in the criteria parameter (e.g. criteria=97.5)
- classify.rf - improved output
- make.contigs - added findex and rindex parameters
- unique.seqs - segfault with count file containing group info. - fixed 1.31.1
- get.seqs - dups=f, renaming issue, https://forum.mothur.org/viewtopic.php?f=3&t=2371. - fixed 1.31.1
- make.contigs - https://forum.mothur.org/viewtopic.php?f=3&t=2451 - fixed 1.31.2
- sffinfo - when parsing an sff file using an oligos file mothur did not adjust the index offset and index length values in the common header.
- get.communitytype order of sample names was not correct in .mix.posterior file if the shared file was not sorted.
- metastats - generate p values for sparse data using fisher’s exact test instead of permutted values
- split.groups - not splitting properly with a count file.
- make.contigs - if file option is used with group provided, and one or more files contain less good reads than number of processors, group assignments were incorrect. - https://forum.mothur.org/viewtopic.php?f=4&t=2571&p=7025#p7025
- trim.seqs - if primer length + barcode length + pdiffs + bdiffs > sequence length, mothur crashed. Sequence should be scrapped.
- shhh.flows - sequences longer than 1024 caused crash on linux.
- make.biom - segfault with multiple labels in shared file. - https://forum.mothur.org/viewtopic.php?f=4&t=2585&p=7072#p7072
- screen.seqs - for count tables without group information, mothur was not creating the *good.count_table correctly. Which could cause fasta/count file mismatch errors downstream.
- removed -m64 flag from makefile for linux
- moved lookup file default position to pathToMothursExe/lookupFiles/LookUp_Titanium.pat - https://forum.mothur.org/viewtopic.php?f=4&t=1366&sid=7f52c79920891f1532992c30f8fe6a3a&start=10
Changes to wiki
- Added ITS database from Segre Lab
- Updated the greengenes-formatted databases
- https://forum.mothur.org/viewtopic.php?f=4&t=2508&p=7147#p7147 - Preferences file menu option not working. Preferences file overwriting references.
- when set.dir command was used logfile path name caused “Could not open” error.