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gbouras13 / plassembler

Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
MIT License
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Two chromosome contigs in Klebsiella pneumoniae 'chromosome.fasta' file #55

Open ayoraind opened 2 months ago

ayoraind commented 2 months ago

Hi @gbouras13,

Thanks for your wonderful tool. I noted that there were two choromosome contigs in more than one 'chromosome.fasta' files following hybrid assembly. I included the --keep_chromosome argument in the command used. I expected to find only one contig in all the 'chromosome.fasta' files generated, and this was so in majority of the cases. However, in a few instances, I see two circular contigs. Is this normal, or do I simply choose the largest contig in this case, since K. pneumoniae is expected to have just one chromosome (that is, one contig)?

gbouras13 commented 2 months ago

Hi @ayoraind ,

Are these two circular contigs around the chromosome size? If they are, then yes, this is expected and suggests your input sample is probably a mixed culture and that you have 2 different bacteria that were sequenced. If not, please give me some more details, as it would be a bug with Plassembler :)

George

ayoraind commented 2 months ago

Thanks @gbouras13 for your prompt response. One of the circular contigs (3.7 - 3.8 Mb) is closer to the expected chromosome size (~ 5.5 Mb) than the other (1.7 - 1.8 Mb). I will run Plassembler again to see if I observe the same results or not.

gbouras13 commented 2 months ago

My guess is that that isolate didn't quite assemble completely, or there is something weird happening with the Flye assembly, given the combined lengths are about 5.5Mb - which shouldn't affect the Plassembler plasmid results, but would be affecting the chromosome assembly perhaps.

Also, if you are using these chromosome assemblies - may I suggest my tool Hybracter (https://github.com/gbouras13/hybracter)? It might be what you want all in one.

George

ayoraind commented 2 months ago

Thanks. I will use Hybracter and keep you posted.

ayoraind commented 2 months ago

Hi @gbouras13

Using Hybracter, I observed that the two contigs were classified as non-circular in one strain. In the other strains, the smaller contig was classified as a plasmid (although I suspect that the smaller contigs should have been classified as chromosome contigs since the size is quite high ~1.7 - 1.8 Mb).