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Three pipelines GenEpi+DTK
1. Layered modular (CoTransmission): Scenario and Scientific Question (What's the isolated contribution of stochastic genotype seed replicates to the variance in genetic fea…
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
v1.1.2
### Workflow Execution
EPI2ME Desktop (Local)
### Other workflow execution
_No response_
### EPI2ME …
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We need to stress test the database with synthetic data to assure it will scale.
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As of 2021-02-26 we have a max_mutation_parents value of 129, which is clearly pathological. Investigate.
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@tanaes wrote
We're planning on modifying the downstream sample demultiplexing pipeline to automatically filter out human reads from human-derived shotgun sequencing. This should be able to be done …
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From Allison Heath and Eric Wenger:
Good morning, quick question on what the Ontology WG recommends for c2m2 OBI id's in several cases where we are not seeing matches.
Kids First data has several…
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**Describe the bug**
SARS-CoV-2 variant BA.2.86 frequently has a 12 basepair insertion in Spike protein, which should be called as
MN908947.3 21608 . GTTAA GTCATGCCGCTGTTTAA
Ho…
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### Ask away!
I have observed an error with the sequences of the inserts in the FASTA format: {{ alias }}.insert.fasta. I investigated the issue and it appears to originate from the following code …
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>>
>> https://github.com/rmcolq/pandora/blob/815da22867f2bdaa3e3bf40f382be830c1506b0a/src/estimate_parameters.cpp#L217-L231
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>> In particular https://github.com/rmcolq/pandora/blob/815da22867f2…
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Hey, great tool!
I wonder if it is also possible to use more than one primer pair? The example primer FASTA and the description sound like one can only use one primer pair. But what if I sequenced …