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fmalmeida/mpgap v3.2.0
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@fmalmeida fmalmeida released this 06 Mar 18:13
· 18 commits to master since this release
v3.2.0
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Learn about vigilant mode.

Release notes

  • Update unicyler to v0.5.0
  • Adjust Pilon polishing module to select how many rounds of polishing to run. Default is 4.
  • Adjust raven module to allow pre-set -k and -w values for corrected/high-quality longreads, while allowing user modification
  • Increase default --max_memory value to 20.GB.
  • Added to parameters to allow users to quickly update how many resources the first attempt of an assembly task should ask
    • --start_asm_cpus
    • --start_asm_mem
  • Add a directory called final_assemblies in the main output directory holding all the assemblies generated in the pipeline execution.
  • Updated documentation as discussed in [#58] and [#57].
  • [#50]
    • Parameters --skip_pilon and --skip_polypolish added to the pipeline
    • MultiQC report was fixed and enhanced
    • Docker image was also modified to download BUSCO standalone and pipeline perform the BUSCO standalone run instead of via quast.
  • [#53] - Include hifiasm assembler in the pipeline. Long reads only and hybrid strategy 2.
  • [#61] - Add a simple parameter to adjust how many cpus and how much memory should the assembly jobs request in the first attempt to avoid lack of resources errors.
  • [#66] - Include an automated generation of a samplesheet for bacannot pipeline.
  • [#72] - hifiasm is only executed for corrected (or high quality) longreads
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