How to use SPADES assembler to de novo assembly contigs

Question

[201314918]

Hi guys I have Contigs thet were generated true the SPADES assembler I then used mitochondrial genomes to search for contigs that match with my contigs. Now I would like to find out, how can I use the SPADES assembler to join those contigs into scaffolds?. I dont have a feference for my species. I am in need of the command that I need to run in order to do this job.

Thank you

[Asaf]

What is the assembly quality? Why do you need scaffolds?

Answer 1

[Buffo]

SPAdes by default creates a scaffold.fa file in the same output directory