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bcgsc / physlr

:chains: Construct a Physical Map from Linked Reads
GNU General Public License v3.0
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Update README.md #170

Closed aafshinfard closed 3 years ago

aafshinfard commented 3 years ago

Quick instruction on calculating assembly-like metrics for the physical map.

lcoombe commented 3 years ago

@afshinfard - I just wasn't clear looking at this PR - Is generating the map quality stats currently default when running physlr? If so, how would a user run physlr without a reference genome?

aafshinfard commented 3 years ago

@lcoombe So, the user can define a ref or not. It is optional. If the input the ref, then Physlr generates a physical-map and a metrics file and some visualizations. If they don't, then only a physical-map will be generated and they can later generate those other files using the map-quality phony by providing a reference.

lcoombe commented 3 years ago

@lcoombe So, the user can define a ref or not. It is optional. If the input the ref, then Physlr generates a physical-map and a metrics file and some visualizations. If they don't, then only a physical-map will be generated and they can later generate those other files using the map-quality phony by providing a reference.

Great! I think that's how it should be. I think just adding in a relevant example showing launching physlr without a specified reference in the README is still a good idea - because I wasn't sure from just looking at the README.

aafshinfard commented 3 years ago

@lcoombe Good point, I agree, will change the example in the README to come with and without a ref for the physical-map

aafshinfard commented 3 years ago

sorry for the many small changes; it's ready to be reviewd.