LASTZ aligner for HaploMerger

Question

[Mehmet]

Dear all,

I need to check repeat sequences in my genome assembly. For this, first I run RepeatMasker. Then, I want to run HaploMerger tool. But for HaploMerger, I have to run LASTZ tool. I checked the manual of it, but confused. How to use command tool for this?

Thank you

[Michael]

You should also read the manual ;) what is it that confuses you (in detail)?

[Mehmet]

Hi, I have already read many times as I mentioned in my message. For instance, my command was:

lastz target.fa (my genome file) no query file. I also used the action "multiple". I received the error Can't understand "multiple". If I don't put the action "multiple", I receive the error "contains more than one sequence". I want to align my genome file with itself.

[Michael]

Did you check this: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#ex_self I guess the command line could look like

lastz genome.fa[multiple] --self

[Mehmet]

Yes I did, but I received this error

FAILURE: multiple action cannot be used with --lav

(lav has requirements on the order of alignments that would require additional

[Michael]

I haven't tested lastz for a long time, but I didn't say --lav but --self

Answer 1

[Chris Fields]

HaploMerger has batch scripts which run lastz for you. The HaploMerger manual (which comes with the distribution) details this.