We are happy to announce the release of mothur v.1.26.0. We have added a improvements to a number of commands to make them faster and easier to use. We’ve also added several new commands for you to try out. Of particular note is get.coremicrobiome, which will tell you how many OTUs are observed in varying numbers of samples for different relative abundance cutoffs. Although this has been a popular concept with the human microbiome research, it can certainly be applied to other environments as well. We are busy working on a number of other commands behind the scenes that we hope to release over the next few months. Specifically, we’re working on SOPs for Illumina, IonTorrent, and PacBio, implementing machine learning algorithms, a new classifier, and more. Stay tuned!
Also, people frequently ask how we describe our analysis pipeline and how we analyze data in general. Of course plagiarism is the Worst Possible Thing In Science, our most recent paper may inspire you. It’s hot this summer in Michigan with hardly any rain. All of this makes it hard to keep the ideas flowing. Be sure to keep your hydrating substances flowing.
- get.coremicrobiome - determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances
- list.otulabels - lists otu labels from shared or relabund file.
- get.otus - can be used with output from classify.otu, otu.association, or corr.axes to select specific otus
- remove.otus - can be used with output from classify.otu, otu.association, or corr.axes to remove specific otus
- load.logfile - extracts current file names from a logfile
- phylo.diversity - improved speed
- set.dir - added debug parameter
- Catchall, get.seqs and classify.seqs commands - added debugging information to the output
- shhh.flows - added large parameter
- rarefaction.shared - added design, sets and groupmode parameters
- otu.association - added metadata parameter.
- rarefaction.single - changed output format
- chimera.uchime - mothur will now look for uchime in your path, if it is not found with mothur.
- Catchall - mothur will now look for catchall in your path, if it is not found with mothur.
- added buffered reads to improve the speed of reading name, taxonomy, design, accnos and group files.
- added phylip as an output format for commands that output distance matrices.
- create.database - added shared parameter command.
- count.seqs - added make.table alias
- count.seqs - added large parameter to to create counts table without loading files into memory
- shhh.flows fixed output file location - https://forum.mothur.org/viewtopic.php?f=3&t=1570&p=4131#p4131
- shhh.flows - added checks to make sure all flow files are completed when multiple processors are used. - https://forum.mothur.org/viewtopic.php?f=5&t=1599
- shhh.flows - is producing an output file called *.flow.fasta instead of *.fasta. Also when using outputdir with the file option, it puts the shhh.fasta and shhh.name files in the wrong folder.
- make.biom fixed bug that occurred if some taxonomies had confidence scores and others did not. - https://forum.mothur.org/viewtopic.php?f=4&t=1585
- Catchall - https://forum.mothur.org/viewtopic.php?f=4&t=1569 - The catchall executable name released with mothur contained ‘C’ instead of ‘c’.
- classify.otu bootstrap values for “unknown” taxon too high - https://forum.mothur.org/viewtopic.php?f=4&t=1588
- align.seqs - align=blast caused segfault
- sffinfo - reported error when ‘~’ was in sff file name.
- classify.seqs - output taxonomy name missing tag when reference taxonomy file does not have 3 parts. - https://forum.mothur.org/viewtopic.php?f=4&t=1613