The best tool for Scaffolding

Question

[davidmaimoun]

Hello, I would like to know if somebody can you advice me to choose the best scaffolding tool (for bacterial genome)?

I get contigs from Spades, and would like use the assembly with nextstrain for snp analysis

Thank you

[dthorbur]

Can you provide more information on what data you have? Chances are without something like optical mapping, high quality long read data, and/or Hi-C, you're only going to get a contig level assembly.

Also, there is nothing stopping you from SNP calling with a contig level genome, but if made up of lots of small contigs you will lose a reasonable amount of data.