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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 19 hours ago

ayoraind commented 19 hours 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 19 hours 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 19 hours 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 19 hours 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 19 hours ago

Thanks. I will use Hybracter and keep you posted.