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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Assembly order #185

Open sejmodha opened 9 years ago

sejmodha commented 9 years ago

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

skoren commented 9 years ago

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.

weihongying commented 7 years ago

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?

skoren commented 7 years ago

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.