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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
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Singe-end analysis - requested enhancement #87

Open AroobAlhumaidy opened 1 year ago

AroobAlhumaidy commented 1 year ago

Hello everyone,

Describe the solution you'd like I would like to ask if the pipeline could work on a single end reads instead of a paired end read, or at least both.

Thank you

Best, Aroob

jvhagey commented 1 year ago

Hi @AroobAlhumaidy what platform are you using for sequencing? This change would be a bit of a project and we aren't going to be able to work on this for the foreseeable future as we prioritize requests from labs that are part of the AR Lab Network. You can make a fork and submit a PR for us to review though. If you reference your fork in this issue others interested in this might be willing to help. If we get more interest in this request I can revisit its prioritization. Currently, there have been more requests for assistance with long read/hybrid analysis than support for single end reads.