What the difference between GenomeAlignmentTools and make_lastz_chains

[981Hao]

Hi,
I see the GenomeAlignmentTools and make_lastz_chains all generate the clean chains through the lastz and kent utilities, so if i want to do multiz or pecan in next step, is all results ok? or which results is best for next step?
Thank you so much

[981Hao]

And I also read your make_lastz_chains, it's do partitions first, can I use multiple parameters in lastz instead to make lastz run faster

[MichaelHiller]

For multiz, you need to convert the chains (from make_lastz_chains) into nets using axtChain and then ideally filter them with the perl script. Pls see the publication for details.

You can likely manually stop after the partition step and then use different parameters for different chunks. But the make_lastz_chains workflow can't do that.

[981Hao]

Dear Hiller, thanks for your reply.