Minimap2: PAF2delta conversion

[jelber2]

Hi,

I am trying to replace a nucmer step (whole genome alignment) in a pipeline with minimap2, where the original pipeline uses the delta file from nucmer4, which is taking far too long [75 cores, 378GB ram, over 4 days]. Is it possible to convert the PAF format from minimap2 to delta format?

[lh3]

Is it possible to convert the PAF format from minimap2 to delta format?

It is technically possible but will need some work. I am not going to write it. If that is your pipeline, it would be good to change it to work with minimap2's PAF format.

[jelber2]

Thank you. It would be rather difficult to modify this pipeline as it uses AMOScmp (http://amos.sourceforge.net/wiki/index.php?title=AMOScmp), but I will look into writing a PAF2delta converter.

[songtaogui]

Hi, @jelber2
I was also looking for a PAF2delta converter.
Have you successfully convert PAF to delta and could you share the scripts?
Thank you very much.

[jelber2]

Sorry @songtaogui, I was able to optimize nucmer and didn’t write any scripts.

[songtaogui]

@jelber2 Thank you for the reply. I will find another way.

[harish0201]

@jelber2 @songtaogui

Currently the easiest way to obtain a delta file is to get the mapping in SAM and then using sam2delta from RaGoo repo. (Shoutout to @malonge)

The only issue is that the sam might take lots of space, but that's the tradeoff :)

[malonge]

Yes I have a python script that goes from SAM to delta. It is tested and should work.

I also have a script that goes from PAF to delta, though it failed my tests and I am not sure why. For the most part, it looks fine, but I think I am having problems with the number of mismatches.

Maybe you can use that as a starting point.

[gorliver]

@harish0201 @jelber2 @songtaogui
I have a perl script can convert paf to delta, it requires the "cs" tags in the paf file.
https://github.com/gorliver/paf2delta

[malonge]

Hi - I forgot about this thread. I now have tested utilities for paf <--> delta as a part of RagTag

ragtag.py paf2delta

or

ragtag.py delta2paf