iMetAMOS

iMetAMOS supplementary data

iMetAMOS

iMetAMOS is a workflow within the metAMOS package starting with version 1.5.
  • To install metAMOS, use either the frozen binaries for metAMOS or run:
    INSTALL.py imetamos
  • Source code and releases are available at the metAMOS github. website
  • Documentation is available at the metAMOS documentation website.
    • If you encounter issues or have questions, please contact the authors of the pipeline:
      Sergey Koren (sergek AT umd.edu)
      Todd J. Treangen (treangen AT gmail.com).
  • For known issues, please see the known issues wiki page.

Example output for GAGE-B R. sphaeroides dataset

  • Example output can be viewed here.
  • Full Postproces/out directory can be downloaded here
  • To reproduce the analysis run:
    initPipeline -d gageb -W gageb_example
    runPipeline -d gageb –p 16

Supporting Data

  • Download the 225 Mycobacterium dataset here
  • Download assembly statistics and runtime information
  • To reproduce the analysis for a given sample (for example ERR233346) run:
    initPipeline -d ERR233346 -W iMetAMOS -1 ERR233346
    runPipeline -d ERR233346 –p 16 -a spades,masurca,velvet

    For a paired-end sample (for example ERR234097) run:
    initPipeline -d ERR234097 -W iMetAMOS -m ERR234097 -i 200:800
    runPipeline -d ERR234097 –p 16 -a spades,masurca,velvet