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2.2.0 - Yesod
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@transcript transcript released this 12 Mar 20:11
· 57 commits to master since this release
2.2.0
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Learn about vigilant mode.

Decent sized update, includes some improvements courtesy of Sebastian Renaut (seb951):

  • Multithreading added for Trimmomatic, PEAR, SortMeRNA
  • The script automatically creates a checkpoint file. Once a step is finished, it writes the name of that specific step in checkpoint and that step is skipped on a rerun of the master_script. This is done to avoid re-running CPU-intensive steps if unnecessary.
  • A new version of the master script now exists, called "master_script_preserving_unmerged.sh". In this script, in the merging step, unmerged reads are concatenated and added to a single file. The forward read and the reverse (complement) read are concatenated with a string of 20 Ns in the middle: This is done through a new R script entitled: combining_umerged.R
  • Extra care is taken to remove unnecessary files once a step is performed to keep disk usage at a minimum.
  • Each step contains an exit statement to be printed if the master script dies due to an unforseen error.
    Trimmomatic removes adapter contamination according to a specific fasta file.
  • All options, read & program location are to be specified in the first section of the script.
  • The script is formated to be run on a HPC using a SLURM job scheduler, but this can be easily changed / removed.
  • The flag --num_alignments 0 in the ribosomal sortmrna step has been removed. This caused problems and slowed things down a lot. Plus, we don't care about the rRNA alignments - whether a sequence aligns to 1 or 1,000 rRNA, it's out anyways...
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