Multiple samples for one assembly with spade

Question

[tans0307]

Hello there,

I am trying to do an assembly with multiple samples using the spade software. The samples are paired-end reads and I will just like to get one scaffold from these samples. Will appreciate any feedback on how I can do so!

Thank You.

[GenoMax]

Reference link for a potential asnwer: C: How to run a set or batch of genome assemblies at once in one go?

[tans0307]

Hello @genomax2, the link that you provided is more for multiple assemblies.

These samples are replicates but are expected to have slight variation. Should I proceed with the cat?

[GenoMax]

It would not be appropriate to gzip/cat different samples into combined file(s). If the files in question are replicates of the same sample then it should be ok.