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Two chromosome contigs in Klebsiella pneumoniae 'chromosome.fasta' file

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
bioinformatics

Research direction

Start by tracing how the --keep_chromosome argument produces chromosome.fasta during hybrid assembly, then reproduce the reported case with Klebsiella pneumoniae and two circular contigs. Done means determining whether multiple chromosome contigs are expected and documenting or correcting the behavior accordingly.

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Description

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)?

Dominant language
Python
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