pipeline for whole genome alignment used in UCSC genome browser

[Fu weiwei]

Hi, UCSC Genome Browser Team,

I would like to use several species for whole genome alignment.

If possible, could you give me the detailed pipeline that your website used?

It would be better if there were command lines about this pipeline.

Thank you very much for your time. Waiting for your reply.

All the best,

Weiwei Fu

 

[Hiram Clawson]

Good Morning Weiwei Fu:

Please note the discussion at:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

This describes the process of using our scripting tool chain that
performs a whole genome alignment. You can view the actual
script in our source tree:

https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/utils/automation/doBlastzChainNet.pl

Note the description of the steps performed by that script:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#How_does_this_process_work

The script can be used in a 'debug' mode, where it will simply write out the
scripts of the various steps but not run them. They can be examined to see
what the details of any step are and can be performed manually.

--Hiram