Draft/Scaffold genome assembly

Question

[netipandey.87]

Does Contig or Scaffold level of bacterial assembly contains plasmid sequences if the genome representation is marked as full in NCBI genome database?? If yes, how to screen those Contigs containing plasmid sequences from rest of the contigs in contigs or scaffold level of assembly??

[lieven.sterck]

not 100% sure on how NCBI deals with this but I would assume it should be indicate somewhere what is included. Gut feeling tells me that in most cases they would refer to the "nuclear" genome and flag the plasmids separate

[Mark]

By full you mean complete? To my knowledge, complete assemblies shouldn't contain any plasmids (or rather a separate contig is designated as plasmid).

For identifying plasmids in draft assemblies, you can use prokka to annotate the assembly. The author suggests this approach:

https://github.com/tseemann/prokka/issues/319

Answer 1

[rajeefa]

You can use plasmidfinder .It works on the contigs fasta file https://cge.cbs.dtu.dk/services/PlasmidFinder/

Answer 2

[netipandey.87]

Thank you everyone...will use the above suggested methods....