mothur v.1.12.0

We are happy to announce the release of mothur_v.1.12.0! As many of you will probably be scurrying to pull posters together for ISME in August, we hope that this release will help you present your data in the best possible light.

This release has three new commands, which will now enable you to take your data directly from a 454-Roche sequencer all the way through your analysis. In other words, we have implemented a command - sffinfo - that will take an sff file and translate it to a text, fasta, or quality score file with any operating system. In addition, we have added two other commands including one to unalign sequences and to find the relative abundance of OTUs. We implemented several ways of normalizing count data and if you have suggestions for others, please let us know. In addition to these three new commands we have added a number of features to the existing stable of commands, which should make your life a bit easier and your analysis more flexible. Perhaps most important, we have fixed a number of bugs that people have communicated to us via email and the forum. Along with providing new alignment and taxonomy reference files containing nearly 15,000 diverse sequences we are in the process of modifying our example analyses to reflect our current thinking about how to trim data based on quality scores and implement all of the new features we’ve released in the last several months.

As always, you can feel free to shoot us emails at mothur.bugs\@gmail.com, post any problems or praise at the forum, and “like” us on facebook. We look forward to your continued support, suggestions, and questions.

New commands

• degap.seqs - a command that takes in an aligned file and spits out a degapped file - ng.fasta
• get.relabund - find the relative abundance of an OTU
• sffinfo - a command to extract a sequence reads from a .sff file.

Feature updates

• made chimera commands able process multiple files and added checks to chimera.pintail to look for conservation and quantile files if they are not given.
• made read.otu sort the shared file alphabetically based on groups
• added ordergroups parameter to read.otu - enter a file that contains groupnames in the order you want
• made mothur insensitive to extra spaces in between the sequence name and sequence group in a groupfile.
• added groups option to get.oturep command. - https://forum.mothur.org/viewtopic.php?f=5&t=219&sid=90e7a96c678e887e09bc1d8a37c34052
• mods to trim.seqs:
  • made it optional to give a name for the forward primer
  • warned if the same barcode is used twice
  • split samples using primer if a primer name is given
  • also trims and splits the qual file if it is provided
  • added two additional options for quality trimming based on a rolling average and a sliding window
• added confidence intervals for thetayc
• You can now set a default path at compile time - https://forum.mothur.org/viewtopic.php?f=5&t=493&sid=cb4f1276fa6bfc534be4a3d024628e5a
• you can now set the frequency as a percentage for the collect, and rarefaction commands. https://forum.mothur.org/viewtopic.php?f=5&t=402&sid=754ff6ec088428a5dcce50ed1e307d70
• added tempdefault parameter to set.dir to override the default set at compile time.

Bug fixes

• made looking for “barcode”, “forward”, “reverse” in oligos file for trim.seqs case-insensitive and give error if something else is entered.
• removed blast-related files after running chimera.slayer with blast search mode.
• in filter.seqs if a filter setting is defined by the user (e.g. hard, trump) then turn off the undeclared, default settings
• fixed bug with nearest neighbor cluster
• fixed bug that was causing double commas in the list file with mgcluster command

Other stuff

• updated the SILVA reference files for aligning and classifying sequences