Providing a precomputed PAF file for scaffolding

[mrvollger]

Hi,

Is it possible to provide a precomputed PAF (or sam/bam if PAF doesn't work) file for scaffolding? Sorry if I missed this in the docs somewhere.

Thanks!
Mitchell

[malonge]

Thanks for asking - yes that is possible! Though it’s a bit of a hack.

Make the output directory in advance (“ragtag_output” or whatever you set -o to). Then, copy or link the PAF file to the output directory. Just make sure that it is named ragtag.scaffold.asm.paf. Ragtag will see that the file is already there in the output directory and it will proceed with those alignments.

One can also use a delta file instead of a PAF file (ragtag.scaffold.asm.delta). If you provide a delta file, just add --aligner nucmer to the command so that ragtag knows to look for a delta file. Here's an example:

mkdir ragtag_output
cd ragtag_output
ln -s /path/to/alns.paf ragtag.scaffold.asm.paf
cd ..
ragtag.py scaffold ref.fa query.fa

Let me know if I can clarify anything.

Thanks
Mike

[mrvollger]

This is perfect! Thanks.