Submission of SPAdes output (scaffold.fa) as contig or scaffold?
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4.2 years ago
nadal-t ▴ 20

Hi folks,

I am sorry for a very basic question. I sequenced a fungal genome with MiSeq (2*300) and I now finished a draft genome assembly with SPAdes (scaffold.fa). From the name, I understand it is assembled to scaffold level but it is very similar to another SPAdes output (contig.fa) although it has better stats. I am going to submit the genome to EMBL, and I can't make up my mind if it is OK to submit it as contig instead of scaffold? The genome is solely built on one paired-end library without mate-paired one.

Thanks in advance for advices.

Assembly genome • 969 views

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