We have an exciting new release of mothur for you with the release of mothur v.1.35.0!
There are several important sets of updates that you will certainly want to know about. First, with this release, you can now use mothur to generate the files needed to submit 454 and Illumina amplicon data to the Sequence Read Archive at the NCBI. That can be achieved using the get.mimarkspackage and make.sra commands. To learn more about how to pull this off you’ll want to follow the tutorial at Creating a new submission. We have been working with the SRA curators to make sure that all of the formatting is right. There may be a few bumps in the road as this is rolled out and people start to use it, but we’re pretty confident that it is working. I’ve even been able to seamlessly submit data from our lab. We’ve tried to make it as painless as possible, so let us know if there’s anything more we can do to make the process easy. Second, we have rewriten the implementation of make.contigs. This update significantly increases the command’s speed. We’ve also implemented the alignment methods implemented in PandaSeq and their methods for calculating quality scores. We still think the default settings in make.contigs are the best, but have gotten enough requests that we thought we’d include them in the new version. Third, using the set.dir command you can now set the seed for the random number generator. This is important for improving the reproducibility of your results between runs that involve generating random numbers. Fourth, for those of you that are fans of the command line-based approach for interfacing with mothur, you can now temper the amount of output that comes to the screen, output the help information, and get the version number for the executable of mothur that you are using using several new command line options. Finally, for those of you that like to dig a little bit into the weeds, we have restructured our GitHub repository and are making greater use of their issue tracking tools to organize our development process. As always, there are a number of other feature updates that we have made as well as numerous bug fixes that you have called to our attention. As always, please continue to bring to our attention any problems you are experiencing in mothur and any ideas you might have for new features or improving your interaction with the software.
In closing, I will be hosting an R workshop for microbial ecologists this May 3-5 in the Detroit area. Let me know if you have any questions. This material is great for taking output from mothur to generate publication quality figures and leveraging the powerful tools that R developers have created for doing statistical and ecological analyses.
- get.mimarkspackage - create blank mimarks package form for sra command (see Creating a new submission)
- make.sra - create submission ready files (see creating a new submission)
Added common command line options. Can now use -q or --quiet, -h or --help, -v or --version.
- set.dir - added seed parameter to allow the user to set the seed for the random number generator
- make.contigs - improved speed, added pandaseq-based quality score data, added kmer aligning method
- cluster.split - allows one to use the cluster.classic option if they set the classic option to T. This is likely the most ideal opetion for people using tax level 5 or 6.
- make.biom - added relabund file as input.
- pcr.seqs - added fdiffs and rdiffs comments
- cluster, cluster.split, cluster.classic, phylotype, mgcluster - Clustering commands did not include the count file info. when printing list file OTU order. Only effects clustering commands. *.pick commands must preserve otuLabels order. - https://forum.mothur.org/viewtopic.php?f=3&t=3460&p=10483#p10483
- classify.tree - added output parameter. Output=node or taxon. Default=node. Output=taxon will label tree with consensus taxonomies.
- get.coremicrobiome - the abundance option can now accept float values. abundance=1 or abundance=0.01 produce same results. Abundance=0.005 or other values between 0 and 1, instead of the 1% as the lowest value.
- chop.seqs - added keepn parameter. Default=f.
- Restructured source files on github for easier downloads and builds.
- cluster.split - MPI version compile issue, https://forum.mothur.org/viewtopic.php?f=4&t=3453&p=10073#p10073. fixed in 1.34.1.
- summary.seqs - multiple processors Windows. fixed 1.34.2
- summary.seqs -MPI bug https://forum.mothur.org/viewtopic.php?f=4&t=3465 - fixed 1.34.2
- pcr.seqs - use of mothur’s paired primer tag instead of forward and reverse tags causing improper trimming. - https://forum.mothur.org/viewtopic.php?f=4&t=3482. fixed in 1.34.3.
- sffinfo - parsed sff files giving corrupt error. - fixed 1.34.4
- pcr.seqs - Windows multiple processors with start and end parameters giving errors. - fixed 1.34.4
- make.contigs - Bug in Windows paralell processing. https://forum.mothur.org/viewtopic.php?f=4&t=3571&p=10466#p10466
- dist.seqs - bug introduced in 1.34.4 - https://github.com/mothur/mothur/issues/46</a>
- rarefaction.single - returning median instead of mean. https://forum.mothur.org/viewtopic.php?f=3&t=3484
- make.contigs - skipping groups if invalid fastq files provided. - https://forum.mothur.org/viewtopic.php?f=4&t=2571
- make.contigs - bug that required barcodes to process
- metastats - infinite loop.
- pcr.seqs - When sequence length < primer Length + pdiffs, basic_string error occurred. Rare case.
- mothur will now read over null strings to avoid pesky sequence not found errors.
- v.1.35.0 is available on github