Michael Alonge

Thanks for the info. This python implementation is not very memory efficient and short read alignments can use quite a lot of memory. If you don't have access to a...

I would use [seqtk](https://github.com/lh3/seqtk)

Hi there, RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag RagTag uses pysam for read-mapping validation, thus dramatically decreasing the memory requirements. Thanks

Hi there, With respect to the assembly size, the RaGOO scaffolds should just be an ordering and orienting of the input contigs. What was the total assembly size for the...

As a general rule, I would do what the [VGP](https://www.biorxiv.org/content/10.1101/2020.05.22.110833v1 ) is doing ([github](https://github.com/VGP/vgp-assembly)). I believe they use a tool called [purge_dups](https://github.com/dfguan/purge_dups). That said, these methods may not work as...

Hi there, Thanks for the suggestion. This was on my list of features to add to v2 and I have implemented a prototype in my development code. Unfortunately, I haven't...

Hmm that is interesting. Firstly, yes you can still use ragoo.fasta. The SV calling step is independent. I am not sure why Minimap2 is running out of memory. For debugging,...

At this point, if you would like to call SVs, I suggest you do your SV calling manually. You can either use minimap2/paftools or nucmer/assemblytics. If you use paftools, you...

@mictadlo glad to hear you have resolved it. @lucventurini absolutely thanks so much for contributing.

Hi there, I am currently working on v2, which uses pysam to dramatically reduce the memory requirements. In fact, the memory for small and large genomes should be roughly the...