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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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option to exclude reference sequence from Augur_PHB #381

Closed jrotieno closed 3 months ago

jrotieno commented 3 months ago

:cool:

:pushpin: Explain the Request

An optional argument to include or not the reference sequence used in Augur_PHB

:books: Context

At the moment, when a user runs Augur_PHB, the reference sequence associated with the organism is by default included in the tree output. This can be problematic when looking at recent and very similar sequences, resulting in an oddly looking tree with a long branch for the reference. Esentially, this reduces proper resolution of sequences of interest.

:chart_with_upwards_trend: Desired Behavior

Ability to remove the reference sequence when need be. Can be a Boolean, true to remove referece abd false to retain reference (default).

:information_source: Additional Information