duplicate sequence names

[try-hunter]

Hello, I encountered an issue while using SPAdes.
I have 10 paired-end samples, and after assembling them individually with SPAdes, I concatenated the 10 scaffold files together using cat. However, I’m concerned that this might cause conflicts due to identical sequence names.
Is there a way to ensure that each sequence has a unique name to avoid conflicts?
Or does the program provide any options to handle this?

[asl]

SPAdes output format for contigs / scaffolds are here: https://ablab.github.io/spades/output.html#contigs-and-scaffolds-format

Indeed, there might be duplicate names, so you need to rename scaffolds to include e.g. sample name. Or invent some other scheme.

There might be multiple ways to do this depending on your habits and / or scripting skills. You can e.g. use sed to replace NODE_ in the header with sample id. Or you can use bioawk, etc.