Hey mothur users,
We’re happy to announce the long awaited v.1.37.0! There are some pretty sweet features in the new release that I’d like to highlight for you. First, for the mac and unix users, we’ve added two methods to cluster and cluster.split to allow you to use abundance and distance-based greedy clustering using the free and open source VSEARCH program. This release was a bit delayed because we’ve been trying to get the windows version to work, but haven’t gotten as far as we’d like. The next release should include it. I would point out that if you are doing 16S rRNA gene sequencing you want to stick with the defaults - this is mostly for those doing ITS. You can see two of our recent papers published in PeerJ and mSystems for more discussion of this. Second, we’ve added a make.file command that will allow you to generate a files file for use in make.contigs. This command should significantly simplify the process of generating the file. Third, we've created a biom.info command that will convert a biom formatted file to mothur-formatted shared and assorted taxonomy files. There have also been a number of other new features and bug fixes that you should check out on the release page.
In addition to improvements to mothur, since the last release we've also published several papers and blog posts that you should definitely check out.
- mothur and QIIME
- No, greengenes' reference alignment hasn't improved
- README for SILVA v123 reference files
- Suck until you don't
- Application of database-independent approach to assess the quality of OTU picking methods
- [De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units](De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units)
- Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
That's all until next time, enjoy! As always, feel free to let us know what you think or if there are additional features you'd like to see in mothur...
- Adds agc and dgc methods to the cluster.split and cluster commands from the vsearch software package. Not available for Windows. #169
- merge.groups - adds count option. http://www.mothur.org/forum/viewtopic.php?f=5&t=3698 #88. Adds method and fasta parameter. Method options are sum, average and median. Default=sum. #105
- get.groups / remove.groups - adds phylip and column options. #79
- get.seqs / remove.seqs - Checks for repeat sequences names and eliminates them. Allows users creating their own templates to easily remove duplicate sequences from their reference files. #159
- Remove MPI source code - MPI version is slower than non-MPI version. No advantage to using it. #144
- unique.seqs - adds format parameter. Options are name and count. #125
- Simplify makefile #157
- make.file - adds numcols parameter. Options 2 or 3. Default=3, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first '' or if no '' is found then the root of the forwardFastq filename. #162
- Output number of warning and errors detected.
- rename.seqs - adds file, map, qfile and contigsreport parameters. The map file allows you to revert sequence names back to original. Works with make.contigs to automatically rename sequences. #132
- make.contigs - adds rename parameter, default=t. Renames sequences to reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream. Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time. #132
- classify.seqs - Changes cutoff parameter default to 80. This change in the bootstrap threshold reflects the default values in the 454 and MiSeq SOPs. #192
- get.current - Adds current RAM usage and total RAM available.
- Replaces '-' characters in sequences names with '_' characters to avoid downstream issues. #205
- Changes default on minlength to 10 for the screen.seqs command. #160
- Removed load.logfile command. Added output file to get.current and input/output file to set.current . These changes allow the commands to work together to keep track of current files between instances of mothur in a more direct and easy to edit manner. You can input the output file of the get.current command into the set.current command using the new current parameter.
- Adds includescrap parameter to the make.sra command. Default=True. http://www.mothur.org/forum/viewtopic.php?f=3&t=3750&p=11122#p11122
- get.otulabels removed. Functions added to get.otus command.
- remove.otulabels removed. Functions added to remove.otus command.
- Adds output and printlevel parameters to classify.seqs, classify.otu, biom.info and summary.tax commands. Output options simple and detail. Default=detail. #204 #158
- Adds relabund parameter to classify.otu command. #101
- Adds threshold parameter to summary.tax command. #31
- Adds parent taxons to unclassified taxons for outputs of classify.seqs, classify.otu, biom.info commands. http://www.mothur.org/forum/viewtopic.php?f=3&t=3183&p=9003#p9003 #29
- Adds count parameter to get.sharedseqs #133
- filter.shared - modifies rareOtus label to prevent mothurConvert error. #137
- make.contigs - File mismatch error with certain sequence name formats and multiple processors. Three column format gz file not producing group file.
- Fixes mothurConvert error if "seed" was part of filename.
- Removes OS limit on open files for cluster.split #142
- make.sra - Fastq.info error about no inputs selected when running make.sra with single fastq file and oligos file.
- cluster.split - removes limit on number of files that can be split by cluster.split. Limit caused "[ERROR]: Cannot open yourFasta.xxx.temp" file error.
- "Illegal Instruction" error on Linux machines. Fixed in 1.29.16 release. #179
- Updates Xcode project file to fix collaboration issues.
- Fixes filter.seqs issue where sequences are not the same length by setting default minlength to 10 in the screen.seqs command. #160
- Windows version - if files were used with less sequences than processors specified then empty file error. #195
- Fixes make.contigs name mismatch bug and gives a slight speed boost. #167
- Fixes lefse "Skipping x iter..." warning.