Michael Alonge

Can I ask what your N50 is?

ok that is good to know. well if you are willing to share the data then I can probably debug pretty fast. Otherwise, I will have to think of some...

Ok sounds good. Really, the way it is designed, the `ragoo.fasta` file should have every single input sequence in it. I think I will try to recreate your issue with...

When you add in the contigs manually, what percentage of sequence is localized to chromosomes? And which reference are you using?

Hi there, After testing the code with your data, I believe I understand the problem. When `-C` is invoked, a single file for each of the unplaced contigs is written...

Hi there, I will have to take a look to see how much work would be required to uncomment that line. I will leave it as an enhancement and will...

Hi there, RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag This feature is implemented in RagTag, and will likely not ever be implemented in RaGOO, which will eventually...

It does seem that your chr0 is a little too large. May I ask what genome you are assembling? Also, what is your contig N50?

Am I interpreting this right by observing that you have a contig N50 of 5k? If you have a large number of very small contigs, those are unlikely to get...

Hi there! The alignments used for scaffolding are in `ragoo_output/contigs_against_ref.paf`. RaGOO will not recreate that file if it already exists, so the trick is to replace that file with nucmer...