# Shortbred default parameter inconsistency

**URL:** <https://forum.biobakery.org/t/shortbred-default-parameter-inconsistency/8146>\
**Category:** ShortBRED\
**Created:** [June 16, 2025, 2:41pm UTC](https://forum.biobakery.org/t/shortbred-default-parameter-inconsistency/8146 "2025-06-16T14:41:47Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![MaximilianBaumgartne](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/maximilianbaumgartne/32/3289_2.png) [@MaximilianBaumgartne](https://forum.biobakery.org/u/MaximilianBaumgartne)\
**Post date:** [June 16, 2025, 2:41pm UTC](https://forum.biobakery.org/t/shortbred-default-parameter-inconsistency/8146/1 "2025-06-16T14:41:47Z")

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First of all thank you for providing such amazing tools !

In the current release from shortbred  
in shortbred\_identify.py line 111:

grpParam.add\_argument(‘–consthresh’,default = .95, type=float, dest=‘dConsThresh’, help=‘Enter the consensus threshold for assigning AA's in the family alignments to the consensus sequences. The default is .70. Examples: .60, .70, .80,…’)

The default parameter differs from what is specified in help.  
What would be the default value for this, I did not find anything on the matter. Does it influence the analysis by a lot ?

Cheers,  
Max

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<div class="post-metadata">

**Author:** ![MaximilianBaumgartne](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/maximilianbaumgartne/32/3289_2.png) [@MaximilianBaumgartne](https://forum.biobakery.org/u/MaximilianBaumgartne)\
**Post date:** [June 27, 2025, 5:26am UTC](https://forum.biobakery.org/t/shortbred-default-parameter-inconsistency/8146/2 "2025-06-27T05:26:21Z")

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If someone else is interested in this question:  
I ran shortbred identify to build markers for 5-6000 proteins (after clustering at 85 id) and the recent uniprot90 databse.  
Shortbred identify takes more the double the amount of time to run trough (32 CPUs 2 days vs. 5 days), mainly during the refblast stage.  
Using .70 for ConsThresh results in slightly less markers found (14.7k vs. 15.2k).  
In terms of what proteins are detected when I ran it on the same samples with shortbred quantify the results were very similar.