search

asl / BandageNG

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
GNU General Public License v3.0
116 stars 10 forks source link

Support for nodes larger than 2^27 #143

Closed diego-rt closed 1 year ago

diego-rt commented 1 year ago

Hello,

I'm trying to visualise an assembly of a 30+ Gbp genome and some of the nodes are more than a few hundred megabases. I've realised that nodes larger than 134217728 bp are not processes by BandageNG and neither visualised or included in the statistics under graph information. Is there are chance assemblies with nodes of this size can be supported in the future?

Thanks!!

asl commented 1 year ago

Are you sure you're using the latest version? We do support nodes up to ~1 Gbp (30 bits).

diego-rt commented 1 year ago

As far as I can tell, I am using v2022.09. Or should I try the continuous build?

asl commented 1 year ago

This is very old version. We are using rolling releases since then. The particular change was implemented ~year ago

diego-rt commented 1 year ago

Oh I see! Ok, I will give it a try. And what if my contigs ever surpass the 1 Gb mark? Our chromosomes are 1.5-4 Gb and we are aiming for T2T. I guess that would be difficult to implement?

diego-rt commented 1 year ago

Apologies, you are totally right. It works with the continuous build for macOS.

asl commented 1 year ago

Oh I see! Ok, I will give it a try. And what if my contigs ever surpass the 1 Gb mark? Our chromosomes are 1.5-4 Gb and we are aiming for T2T. I guess that would be difficult to implement?

This is not something we're going to handle as it would increase memory consumption for all users drastically.