How to confirm that a sequence belongs to a specific organism

Question

[lya23]

Hi everyone, I have many doubts about how to confirm that a sequence belongs to a specific organism. For example, suppose that you want to sequence the squid genome but, when the sequence arrived, you notice that only 1% belongs to the squid and the other 99% are from symbionts. How can you identify that 1% of sequences that belong to the squid? Also, you can't compare with other sequences because is the first squid that is sequenced. Finally how can you calculate the coverage?

I hope I have explained well and you understand me. Thank you.

[Ahill]

Are any of the symbionts sequenced, such that you could subtract known symbiont sequences? This paper suggests there are some squid genomes out there, might have some ideas.

[Carambakaracho]

With all due respect, when this is your question

How can you identify that 1% of sequences that belong to the squid?

how did you make the percentage estimate in the first place?

you notice that only 1% belongs to the squid and the other 99% are from symbionts.