After a long delay, we are very happy to announce the release of mothur_v.1.34.0 ! We’re anxious to get back on our normal release schedule of a new version ever month or two. In the current release, we’ve added a new machine learning algorithm classify.svm and added a bunch of new features that you all have requested. There are also a number of bug fixes that have also been incorporated into the release. Some of the feature updates that you might find most interesting is the addition of the shannon range calculator that was published last year in ISMEJ by Haegeman and colleagues and the addition of the Jensen-Shannon Divergence calculator. You may notice that we don’t quite have the make.sra command up and running yet. It’s still very much in the works and we have a lot of the components in place to make it happen. We are working with the folks at the SRA to make it as seem less as possible for you all and so this has required a bit of iteration. We were really hoping to have something for you by this release, but all we can do is hope that we’ll have it for the next release. SRA is very excited about this, but they just need to make sure all their ducks are in a row first.
There’s also a few other things going on that you should know about...
- We’ve launched a blog. Of course, we’re only 10 years behind, but hey! The plan is to use the blog to discuss how to use mothur to do different things beyond the analysis examples and how we generate various reference files. You’ll see a nice mix of mothur, R, and bash commands getting play in the posts.
- There will be a mothur workshop in Detroit from December 17-19. The next workshop will be in March and I’m still not sure whether it will be a mothur or R workshop. Email Pat if you are interested.
We’re plugging away at continuing to make mothur a great program, as always, if you have questions, ideas, or code to contribute, please don’t hesitate to shoot us a note!
- get.mimarkspackage - create blank mimarks package form for sra command
- make.sra - create submission ready files
- classify.svm - Rank OTUs using the support vector machine learning algorithm
- added shannonrange calculator to collect.single, summary.single, rarefaction.single.
- added shared parameter to count.seqs aka make.table command. Can be used to transpose the shared file for use with other software packages.
- consensus.seqs cutoff parameter can now be a float. cutoff=97.5.
- dist.shared - when subsample used *.ave distance matrix saved as current phylip file
- tree.shared - added Jensen-Shannon Divergence calculator, jsd and Square Root Jensen-Shannon Divergence calculator, rjsd. - https://forum.mothur.org/viewtopic.php?f=5&t=2961
- cluster.split - added the file option which allows you to enter your file containing your list of column and names/count files as well as the singleton file. This file is mothur generated, when you run cluster.split() with the cluster=f parameter. This can be helpful when you have a large dataset that you may be able to use all your processors for the splitting step, but have to reduce them for the cluster step due to RAM constraints. For example: cluster.split(fasta=yourFasta, taxonomy=yourTax, count=yourCount, taxlevel=3, cluster=f, processors=8) then cluster.split(file=yourFile, processors=4). This allows your to maximize your processors during the splitting step. Also, if you are unsure if the cluster step will have RAM issue with multiple processors, you can avoid running the first part of the command multiple times.
- make.contigs - added checkorient parameter. - https://forum.mothur.org/viewtopic.php?f=3&t=2993
- fastq.info, sffinfo, trim.flows- added checkorient parameter.
- trim.flows can now process paired barcodes and primers.
- fastq.info stopped processing after 100001 seqs. - https://forum.mothur.org/viewtopic.php?f=4&t=2829 - fixed 1.33.1
- make.biom picrust couldn’t handle unclassifieds - https://forum.mothur.org/viewtopic.php?f=4&t=2816 - fixed 1.33.1
- create.database OutLabel bug - “cannot convert Otu0001 to an integer” fixed 1.33.3
- merge.sfffiles -Windows version caused substring error on parse. fixed 1.33.2 3/11 version.
- chimera.slayer - “[megablast] FATAL ERROR: blast: Unable to open input file” on linux version with multiple processors. fixed 1.33.3
- rarefaction.single - *.groups.rarefaction file labels in wrong order - https://forum.mothur.org/viewtopic.php?f=4&t=2963 - fixed 1.33.3
- align.seqs - Windows align.seqs flip=t caused segfault fixed 1.33.2 3/19 version
- summary.shared subsample issue - https://forum.mothur.org/viewtopic.php?f=4&t=2861 - fixed 1.33.3
- seq.error is changing the current fasta file to the seq file. it shouldn’t change the current fasta file.
- trim.seqs - qaverage bug scrapping seqs - fixed 1.33.3 4/4.
- make.biom - “biom error: cannot convert null to a float”
- get.seqs, remove.seqs, remove.lineage, get.lineage, screen.seqs, pcr.seqs changed read of count file causing file mismatches with count files that didn’t include group data.
- clearcut - distances out of range bug
- dist.shared - https://forum.mothur.org/viewtopic.php?f=3&t=3186
- make.contigs - rindex files - https://forum.mothur.org/viewtopic.php?f=3&t=3159&start=10#p9096