reduce N's in my assembly

[meriem]

hello,
i did de novo assembly using abyss for a bacterial strain (1,6 MB), i got approximatively 600 N's according QUAST results, is it too much for the my genome length? and if so, how can i reduce it?

thank you very much guys

[Brian Bushnell]

600 Ns in an assembly is fine. You can reduce that by not doing scaffolding, but then you'd have a worse assembly. There are also some programs like gapfiller that might be able to reduce the number of Ns.