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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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TBProfiler tNGS workflow #276

Closed sage-wright closed 4 months ago

sage-wright commented 8 months ago

:cool:

:pushpin: Explain the Request

User requested a tNGS workflow that runs (1) clockwork -> (2) TBProfiler -> (3) tbp-parser with potentially read trimming.

:books: Context

tNGS currently cannot be analyzed with the TheiaProk workflows. Since it is targeted data, creation of an assembly would fail as would other modules that are run automatically.

:chart_with_upwards_trend: Desired Behavior

A workflow designed to take raw tNGS M. tb data and return the outputs of tbp-parser.

:information_source: Additional Information

Due by end of January