GCF_030867095.1 chain file generation & question on workflow

[Gordon, Martin]

Hi Gerardo and UCSC team,

Thank you for generating the chain files and pointing out the availability of the genome GCF_030867095.1.

I would like to know a little more about the workflow for generating chain files for future cases. Does your in-house pipeline still follow the workflow outlined here? https://genomewiki.ucsc.edu/index.php?title=DoBlastzChainNet.pl

I have found a nextflow pipeline available that simplifies the process that I am using myself to generate these files. https://nf-lo.readthedocs.io/en/latest/index.html. Have you any experience of using this tool?

Thanks again,

Martin

[Gerardo Perez]

Hello, Martin.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

Yes, we still follow the same workflow outlined in the DoBlastzChainNet.pl wiki. One of our engineers shares that the nextflow appears to do the same procedure and it would be fine to use the nextflow procedure instead of our workflow since it does not easily function in external environments.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute