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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Question Regarding Mob-recon #83

Closed YasirKusay closed 3 years ago

YasirKusay commented 3 years ago

(Sorry if this is not the correct place to post this). While looking for suitable tools for my work, I found this to be relevant to what I need. With regards to Mob-recon, are the contigs in chromosome.fasta in the correct order?

kbessonov1984 commented 3 years ago

Hi Yasir, No problem. We also have contact emails that you can use for questions (james.robertson@canada.ca and kyrylo.bessonov@canada.ca)

Could you please specify if by the "correct order" you mean the same order as in the input fasta file? Why order is relevant in your context?

YasirKusay commented 3 years ago

Hi @kbessonov1984, by correct order, I mean that the chromosome is assembled, piecing together the contigs in the correct order.

YasirKusay commented 3 years ago

On a side note, could MOB-recon (or some other function in this program) perform DNA assembly?

jrober84 commented 3 years ago

MOB-suite doesn't perform any scaffolding so the order is just by contig id number. If you want to order contigs then you could consider a tool like https://github.com/fenderglass/Ragout. Assembly is a completely different process and there are many excellent assemblers available. SPAdes, Unicycler etc. So we will not be building assembly into the MOB-suite