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Task #5055
closed
Idea #3535: Implement upload Genome to Lightning Pipeline
Build Arvados-compatible pipeline to convert FASTJ to CGF
Updated by Sarah Guthrie almost 10 years ago
- Subject changed from Build Arvados-compatible pipeline to convert FJ -> CGF to Build Arvados-compatible pipeline to convert FJ to CGF
Updated by Abram Connelly almost 10 years ago
There has been a proposal to not treat 'low-quality' tiles as separate library tiles. That is, fill in base pair information for tiles that have no-calls in them and have the no-call information be stored on the sample level (on the CGF level).
There is still some question as to whether this will alleviate the library growth due to noise.
Currently, the steps look to be:
-generate a 'consensus' tile that is the average of base pairs seen that location
-from the consensus tile, build the library
-once the library is generated, CGF can be generated.The consensus tile's main motivation is to be used in the base library sequence and can be thought as being chosen to minimize the differences from the consensus tile and the tiles that appear in the population.
Updated by Sarah Guthrie over 9 years ago
- Subject changed from Build Arvados-compatible pipeline to convert FJ to CGF to Build Arvados-compatible pipeline to convert FASTJ to CGF
- Parent task changed from #5001 to #3535
Updated by Sarah Zaranek over 6 years ago
- Status changed from New to Closed
- Start date set to 04/10/2018
- Remaining (hours) set to 0.0
Sarah and Abram built this with the new codebase.
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