We are happy to be releasing mothur v.1.33.0, which includes a number of exciting new features and updates. There is one new command - merge.sfffiles, which does the obvious. Among the new features in existing commands we have added the Square Root Jensen-Shannon Divergence and jensen-shannon divergence calculators, which you can use to calculate distances between samples using “rjsd” and “jsd”. These have been popular in some of the recent microbiome literature and thought you would appreciate having access to these. We have also added the ability to assign samples to community types in get.communitytype using K-means and PAM; however, we still recommend using DMM. Following up on some of the features in the last release that were based on the work of Curtis Huttenhower, we have added the picrust and reftaxonomy options to make.biom so that it is easier for mothur users to interface wihe picrust. Finally, there are a number of odds and ends that you’ll see below .
We hope to have another release out to you in the next month or so with a really important new command. We have been working with the SRA at NCBI to create a mothur command that will prepackage everything to make uploadind data to the SRA easier. Those of you that we have spoken about are very excited about this. The folks at the SRA have been great about faciliating this and understanding the difficulties users are facing in getting their data up to the SRA.
If you haven’t heard, I will be hosting another mothur-based workshop in Detroit on March 24-26. See the workshops page for more information. There are still a few seats available. There will likely be another R workshop in June and mothur workshops in August and December.
Keep your great ideas coming and we’ll do our best to work them into mothur!
Pat PS. I’m now on twitter (\@PatSchloss) and you can feel free to ask mothur-related questions there (in 140 characters or less!)
- merge.sfffiles - combine sfffiles. - https://forum.mothur.org/viewtopic.php?f=3&t=2466
- heatmap.bin - added otuLabels to 1.32.1
- make mothur “smarter” about OTULabels. OTU001 and OTU01 should be the same. - 1.32.1
- list.seqs, get.seqs and remove.seqs - added fastq as an option
- add otulabels to list file
- make.biom - added picrust and reftaxonomy parameters.
- mothur will preserve information after sequence names in a fasta file.
venn - permute parameter can equal 1, 2, 3, or 4.
- get.oturep - changed otu numbers to be labels
- deunique.seqs - added count table - https://forum.mothur.org/viewtopic.php?f=3&t=2673&sid=1df296b80f7a182faa8ebdf54f43122e
- nmds - added group label to *.axes file - https://forum.mothur.org/viewtopic.php?f=3&t=2677
- fastq.info - added oligos, group, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs parameters so you can split fastq files by sample.
- sffinfo - added group parameter so you can split sff files by group
- dist.shared, collect.shared and summary.shared - added Jensen-Shannon Divergence calculator, jsd.
- dist.shared, collect.shared and summary.shared - added Square Root Jensen-Shannon Divergence calculator, rjsd.
- trim.seqs - added logtransform parameter to
- trim.seqs - reorient parameter no longer requires paired barcodes and primers
- metastats, unifrac.weighted, unifrac.unweighted, parsimony, chimera.uchime, chimera.perseus, chimera.slayer, shhh.seqs and pre.cluster: improved work balance load between processors for paralellized commands
- get.communitytype - added dmm, pam and kmeans methods
- get.communitytype - added calc, subsample, iters parameters for calculations in pam and kmeans.
- get.current - added directory information. - https://forum.mothur.org/viewtopic.php?f=8&t=332&p=7824#p7824
- classify.seqs and summary.tax - added relabund parameter. relabund=t outputs relative abundances to *.summary file instead of raw abundances. Default=f.
- chimera.uchime, chimera.perseus, chimera.slayer - with count table and dereplicate=t caused total=0 error message. - https://forum.mothur.org/viewtopic.php?f=4&t=2620. - 1.32.1
- sff.multiple - setting processors=1 for future commands. Not using file redirects in commands it runs.
- venn - fixed bug where command overwrote .sharedotu files when permute=t
- pcr.seqs keepdots=f could cause an aligned template to become unaligned. https://forum.mothur.org/viewtopic.php?f=3&t=2653&p=7354#p7354
- summary.shared - *.ave.dist matrix = 0 when processors > 2 when using the subsample parameter and not using the distance parameter. https://forum.mothur.org/viewtopic.php?f=4&t=2660&p=7372#p7372
- classify.otu - error in *.tax.summary counts with basis=sequence when using a count file. https://forum.mothur.org/viewtopic.php?f=4&t=2492&p=7420#p7420 - fixed in 1.32.0.
- sffinfo - windows version with oligos file - https://forum.mothur.org/viewtopic.php?f=3&t=2555&p=7422#p7422
- set.current - setting processors option to 1, if not set.
- trim.flows - printing trimmed number of flows to scrap file instead of original number of flows. Caused error if you wanted to read scrapped flow file.
- get.oturep - countable caused sequence not found error.
Changes to wiki
- Provided a worked example of why cutoff changes when clustering with the average neighbor algorithm in the FAQ
- screen.seqs - removed requirement of contigs report file. 1.32.1
- added MISeq_SOP Pipelines