search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
750 stars 135 forks source link

Metaplasmidspades contigs that are NOT categorized as "plasmid" #788

Closed ilkaybuysal closed 3 years ago

ilkaybuysal commented 3 years ago

Dear developers,

I'm comparing the plasmid prediction of Metaplasmidspades for known plasmid datasets and would like to calculate True negative(TN) and false negatives for the dataset. Can we reach the contigs that Metaplasmidspades categorized as "non-plasmid"?

Thanks in advance.

asl commented 3 years ago

Tagging @Dmitry-Antipov

Dmitry-Antipov commented 3 years ago

Hi. Metaplasmidspades is not a plasmid classification tool. Plasmid assembly is improved with iterative removal of non-plasmid edges of the assembly graph. So we do not output non-plasmid sequences (not contigs, these sequences are removed before contig generation).

For the plasmid/nonplasmid classification I can suggest to use viralVerify ( https://github.com/ablab/viralVerify ) - it classifies contigs of viral, chromosomal and plasmid origin based on gene content.

ilkaybuysal commented 3 years ago

Hi,

Thanks a lot for the explanatory answer and the suggestion.