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Version 1.38.0

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@mothur-westcott mothur-westcott released this 20 Jul 18:49
· 1596 commits to master since this release

Hey mothur users,

We’re happy to announce the release of v.1.38.0! This release primarily has a bunch of random bug fixes that we were anxious to get out to you. Two new commands should strike your interest. First, we have introduced rename.file, which renames files so that you don't have to worry about using your system commands and updates the "current" files. Second, building off the introduction of VSEARCH functionality in the last release, we've created chimera.vsearch to detect chimeras using VSEARCH. Their benchmarking indicates that it performs similar to UCHIME, which is available as chimera.uchime.

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.


New Commands

Feature Updates

  • Removes hcluster command. It is really really slow and we don't recommend it. #208
  • Removes save option which kept references in memory. #208
  • Removes clear.memory command which worked with the save option. #208
  • Removes pds.pipeline command. #208
  • Command line mode returns exit-code to indicate failure. #151
  • Removes reftaxonomy parameter from classify.otu and #241
  • Removes large parameter from count.seqs command. #203
  • Allows make.biom with picrust option to handle mothur's new parentTaxon_unclassified format. #241
  • Adds mothur's location as a default file location to check. Reduces unable to open file errors. #231
  • Adds count parameter to sens.spec command. #225
  • Clarifies seq.error command output. #175
  • Adds sets parameter to lefse command. #234
  • Removes indexFile requirement for using NONE option in oligos file. make.contigs. #193
  • make.contigs command will skip blank file pairs. #233
  • Warn about illegal characters in group names to prevent downstream analysis issues. #37
  • Adds rdiffs to pcr.seqs command to allow for setting different diffs for the forward and reverse primers. #244

Bug Fixes

  • Mothur can handle whitespace in command lines. #191
  • Fixes gradient bar on heatmap.sim command. #237
  • Fixes bug with classify.otu persample option.
  • Fixes bug with agc method in cluster and cluster.split
  • Fixes bug with command not including name file counts in *tax.summary.
  • Fixes RAM output for linux get.current. #232
  • Error generated when filenames are too long for uchime program. #226
  • Fixes cutoff adjust for agc and dgc clustering methods. #254


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