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Dear all,
I have assembled a few microbial genomes with SPAdes and would like to upload these WGS projects to NCBI. I have searched to see how SPAdes represents gaps vs unknown bases, but I can't find it stated explicitly.
To upload to NCBI as a gapped genome submission, one needs to know the following information:
I know that, for example, for Velvet will represent all gaps less than 10 bases as 10 Ns. Does SPAdes have any sort of rule like this?
Thank you very much in advance for your help.
-Heidi
I have assembled a few microbial genomes with SPAdes and would like to upload these WGS projects to NCBI. I have searched to see how SPAdes represents gaps vs unknown bases, but I can't find it stated explicitly.
To upload to NCBI as a gapped genome submission, one needs to know the following information:
- the minimum number of N's in a row (ie 'run of Ns') that represents a gap
- if any runs of Ns represent gaps of unknown size
- if the sequences also include N's that are ambiguous base calls, then what is the length of the longest run of ambiguous bases. To use these simple instructions, the maximum number of Ns in a row that are ambiguous bases must be less than the minimum number of N's in a row that represents a gap.
I know that, for example, for Velvet will represent all gaps less than 10 bases as 10 Ns. Does SPAdes have any sort of rule like this?
Thank you very much in advance for your help.
-Heidi