The pipeline should understand and adapt for multi-segment viruses, like Rotavirus and Rift Valley Fever Virus.
More Info
Context
The PIs on this project want to be able to analyze Bovine and Porcine Rotavirus and Rift Valley Fever Virus via this pipeline.
Alternatives
Currently, it is possible to analyze these viruses using YAVSAP. You must run the pipeline for each segment, changing the value of --genome to the closest reference of each segment. YAVSAP has changed drastically since the last time this was done, however (See #6), so it might not work anymore.
Possible implementation
This feature will require #23 to be completed.
I think the best way for the user to tell the pipeline the number of segments is via additional columns in the --genomes_list parameter. The new format might look something like
#name
Segment L NCBI num
Segment M
Segment S
Kenya-128b-15
KX096938.1
KX096939.1
KX096940.1
SA01-1322
KX096941.1
KX096942.1
KX096943.1
The problem: when dealing with quasi-species, how can we define subconsensus genotype calls for all segments collectively? Effectively pooling the results for all segments and showing them on The Visualizer will also require more thought.
Summary
The pipeline should understand and adapt for multi-segment viruses, like Rotavirus and Rift Valley Fever Virus.
More Info
Context
The PIs on this project want to be able to analyze Bovine and Porcine Rotavirus and Rift Valley Fever Virus via this pipeline.
Alternatives
Currently, it is possible to analyze these viruses using YAVSAP. You must run the pipeline for each segment, changing the value of
--genometo the closest reference of each segment. YAVSAP has changed drastically since the last time this was done, however (See #6), so it might not work anymore.Possible implementation
This feature will require #23 to be completed.
I think the best way for the user to tell the pipeline the number of segments is via additional columns in the
--genomes_listparameter. The new format might look something likeThe problem: when dealing with quasi-species, how can we define subconsensus genotype calls for all segments collectively? Effectively pooling the results for all segments and showing them on The Visualizer will also require more thought.