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Assembly order

Open sejmodha opened this issue 10 years ago • 3 comments

Hi There,

When multiple assemblers are specified in -a parameter of runPipeline, assemblers are executed in alphabetical order in MetAMOS. Is there a way to change this to run assemblers in the order of names specified rather than alphabetical order?

Thanks Sej

sejmodha avatar Mar 03 '15 11:03 sejmodha

Hi,

Currently there is not a way to overwrite the alphabetical order. Are you trying to examine the output of one assembler before a run completes? I'll leave this open as a feature request for a future release.

skoren avatar Mar 03 '15 17:03 skoren

hi,

When multiple assemblers are specified in -a parameter of runPipeline, all selected assemblers will be run and the best selected for subsequent analysis. It is the operation that "the best selected for subsequent analysis" is defined by software or by user setting?

weihongying avatar Jun 23 '17 07:06 weihongying

The best is defined by scoring all the assemblies and taking a vote, this is described both in the metAMOS documentation for the Validate step: http://metamos.readthedocs.io/en/v1.5rc3/content/directory.html#validate

and the iMetAMOS manuscript: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-126

The criteria can be modified by user parameters if needed.

skoren avatar Jun 23 '17 17:06 skoren