iMetAMOS

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 test_gageb
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