Releases · mothur/mothur

Stops sort of user created list file.
Fixes bug introduced in 1.37 that removed barcodes and primers from fastq files instead of simply identifying samples for make.sra command.
Fixes bug with merge.groups initialization of the shared file.
Cleans up makefile.
Removes extra unclassified level from taxonomy files
Fixes make.contigs gz file error - http://www.mothur.org/forum/viewtopic.php?f=4&t=4210&sid=8303c7614b85114d0587fc03fa3fefce

Assets 6

05 Apr 21:59

mothur-westcott

v1.37.0

a9fa52e

Version 1.37.0

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.

Blog:

Papers:

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...

New Commands

biom.info - reads biom file and creates shared, taxonomy, constaxonomy and tax.summary files. #82

Feature Updates

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

Bug Fixes

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.

Registered Users

3663

Assets 10

29 Jan 14:34

mothur-westcott

v1.36.1

cd70dde

Version 1.36.1

Version 1.36.0 with 2 Bug Fixes

make.file - Linux version only bug. Caused error messages about find command -maxdepth parameter.
classify.rf - Design file change caused results to be all zeros.

Assets 10

23 Jul 18:16

mothur-westcott

v1.36.0

9c754f2

Version 1.36.0

New commands

set.seed - allows you to seed random.
make.file- creates a file containing list of fastq or gz files for input to make.contigs.

Feature updates

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. - http://www.mothur.org/forum/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. - http://www.mothur.org/forum/viewtopic.php?f=4&t=3703
degap.seqs - adds the processors option.
Adds column headers to Design File
phylo.diversity - adds sampledepth parameter. - http://www.mothur.org/forum/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.

Bug fixes

metastats - infinite loop with certain datasets - http://www.mothur.org/forum/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. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3781&p=11241#p11241
sffinfo - off by one in right side trimming. http://www.mothur.org/forum/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.