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Difference between revisions of "Mothur v.1.36.0"

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(Feature updates)
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* [[set.dir]] - Sets tempdefault location to mothur's executable location to help reduce "unable to find file" errors.
 
* [[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.
 
* [[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==
 
==Bug fixes==

Revision as of 14:19, 16 July 2015

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

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