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How to use SPADES assembler to de novo assembly contigs

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

assembly
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updated by Buffo Buffo • written by 201314918 • 201314918

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

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written by Asaf Asaf

1 answer

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

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written by Buffo Buffo

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