We are happy to release mothur v.1.28.0 on the US election day - hopefully we can all agree that this is a good thing! Since the last release we have been busy adding a new command and a number of new parameters that will make our final Illumina pipeline easier to use. If you have interest in using mothur to analyze MiSeq sequence data, please let us know, we’d be happy to have you test our new functions. Briefly, we have a new sff.multiple command that makes life easier for those that get multiple sff files from their sequence provider. We’ve also updated the 454 SOP to reflect some of the recent changes we’ve made to mothur over the past several releases.
If you haven’t already, be sure to check out our latest article, that rebuts a previous ISMEJ article. The piece covers the issue of whether sequence alignment as we do it is necessary. Initial feedback has been very positive. The next several releases promise to be very exciting. We’ll be unveiling a new mothur GUI and pipelines for non-454 sequencing platforms.
As always keep the feedback and citations coming! We were happy to notice that the mothur paper is the 15th most cited paper in AEM history and DOTUR is the 4th. Thank you, thank you, thank you! We appreciate the gifts and flowers you continue to send us. One of the students in the lab would like to see a little more love come our way and would like you all to know that if things don’t improve, we will start posting advertisements in the mothur window..
- sff.multiple - The sff.multiple command reads a file containing sff filenames and optional oligos filenames. It runs the files through sffinfo, trim.flows, shhh.flows and trim.seqs combining the results.
- make.table command modified to create a “.count_table” file. Added large parameter in case files are too large for ram.
- sffinfo - added oligos, pdiffs, bdiffs, sdiffs, ldiffs and tdiffs parameters to split sff files. - https://forum.mothur.org/viewtopic.php?f=5&t=1647.
- added count parameter to cluster, cluster.classic, cluster.split, mgcluster, make.shared, chimera.perseus, chimera.slayer, chimera.uchime, summary.tax, classify.seqs, classify.otu, unifrac.unweighted, unifrac.weighted, parsimony, bin.seqs, phylo.diversity, cluster.fragments, unique.seqs, consensus.seqs, get.groups, remove.groups, get.seqs, list.seqs, remove.seqs, get.lineage, remove.lineage, summary.seqs, summary.qual, align.check, heatmap.sim, trim.seqs, split.groups, tree.shared, screen.seqs, pre.cluster, get.oturep, pcr.seqs, sort.seqs, remove.rare, count.groups, sub.sample and split.abund.
- fastq.info - added format parameter to adapt for different quality score bases.
- classify.seqs - changed name of bayesian method to wang
- amova and homova - added sets parameter - https://forum.mothur.org/viewtopic.php?f=3&t=1777
- make.biom - added metadata parameter - https://forum.mothur.org/viewtopic.php?f=5&t=1786
- otu.association - added cutoff parameter - https://forum.mothur.org/viewtopic.php?f=5&t=1639
- mothur can read sequences with spaces in the sequence string.
- You can have ‘-‘s in a file names as long as they are proceeded by a ‘\’. Example: my-file-name should be entered as my\-file\-name.
- classify.seqs - mothur will ignore sequences present in the taxonomy file, but not in the reference file.
- list file printed with abundant OTUs first
- chimera.uchime - added dereplicate option so one can control whether to remove sequences from all groups if they are flagged as chimeric in any.
- parsimony - name file info was not included in the creation of the random trees which effected significance values.
- fastq.info - negative quality scores. - https://forum.mothur.org/viewtopic.php?f=4&t=1727&p=4651&hilit=fastq.info#p4651
- chimera.uchime - spaces in path causing crash
- classify.seqs - if taxonomy file contained file path information “cannot resolve path for” error was thrown.
- consensus.seqs - cutoff rounding error - https://forum.mothur.org/viewtopic.php?f=4&t=1781
- align.check - added name parameter back in.
- added check to align.seqs to make sure template is aligned.
- clearcut - windows crash reports
- get.lineage && remove.lineage - can handle () in taxon names, https://forum.mothur.org/viewtopic.php?f=3&t=1815
Changes to wiki
- Updated 454 SOP
- count_file which is a combination of the name and group file’s information. Uses less memory and runs faster with mothur’s commands.