We’re excited to announce the release of mothur_v.1.36.0! This release has a number of exciting new commands and features. The new commands include set.seed, which allows you to peg the seed for the random number generator that is used by a number of other commands (e.g. cluster) to improve reproducibility. We’ve also added make.file, which will generate the files file that you use in make.contigs based on the sequence files in your directory. On the new features, there are a number of things we’ve done to tidy up the overall package. More meaningful, however, is that in the mac and linux versions of mothur you can now give make.contigs your uncompressed fastq.gz files as input. We are working on this feature for windows, but ... windows. This should save you a bunch of hard drive space :). We’ve also added a feature to pre.cluster so that you do not need to provide a full multiple sequence alignment. Instead, you can provide it unaligned sequences and it will carry out the typical algorithm but will also do a pairwise alignment. I *think* this will be useful for people doing ITS sequencing.
We have a number of other features on our docket for the next release. As always, don’t hesitate to email us or use the forum to propose new features and commands. As I mentioned in an earlier email, I will be hosting a mothur workshop in the Detroit area in early September, holler if you are interested or have questions.
- set.seed - allows you to seed random.
- make.file - creates a file containing list of fastq or gz files for input to make.contigs.
- pre.cluster - added cluster method for unaligned sequences. Added align, mismatch, match, gapopen, gapextend parameters.
- set.dir - if output directory does not exist mothur will create it for you.
- chimera.uchime - adds method tag to output files. - https://forum.mothur.org/viewtopic.php?f=5&t=3636&p=10748#p10748
- chop.seqs - adds qfile option to allows for chopping quality files.
- classify.otu - adds threshold parameter. The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted.
- rename.seqs - adds count, delim, and placement parameters.
- seed parameter added to all commands to allow you to easily seed random while running commands.
- make.shared - mothur no longer checks for biom matrix type to allow for more flexibility.
- make.shared - rabund files are no longer outputted. mothur will create a rabund file with the get.rabund command.
- set.dir - if output directory does not exist it will be created.
- no longer create a log file simple command line option runs of mothur
- make.sra - allow for assigning multiple sets of files to the same group in 3 column format.
- make.contigs - allow for missing reads in files.
- metastats - remove qvalues. Also removes fortran source from mothur.
- automatically adjust number of processors when fork() fails
- Removes extra white spaces from mothur’s print to make output files more compatible with other software packages. - https://forum.mothur.org/viewtopic.php?f=4&t=3703
- degap.seqs - adds the processors option.
- Adds column headers to design_file
- phylo.diversity - adds sampledepth parameter. - https://forum.mothur.org/viewtopic.php?f=3&t=3320
- set.dir - Sets tempdefault location to mothur’s executable location to help reduce “unable to find file” errors.
- make.contigs - allow for gzipped version for fastq files as inputs.
- Added file parameter to saved files by mothur. file=current can now be used.
- metastats - infinite loop with certain datasets - https://forum.mothur.org/viewtopic.php?f=3&t=3701
- cluster.split - did not allow you to use the classic option with the file option.
- make.biom - repeat labels when combining mothur OTU labels with non mothur OTU labels, this can results in a duplicate “simple” label. This causes an incorrect taxonomy to be assigned to the OTU.
- remove.groups - not creating a list file for each label.
- make.biom - remove paths from filenames to make compliant with qiime parser. - https://forum.mothur.org/viewtopic.php?f=3&t=3781&p=11241#p11241
- sffinfo - off by one in right side trimming. https://forum.mothur.org/viewtopic.php?f=4&t=3764
- make.contigs - Bug Fix - when using index files in version 1.35 quality data was over trimmed by the length of the barcode.