Hi all,
how do I choose a genome to be used as reference if i want to order the contigs once they are assembled?I know that it is supposed to be the most closely related . But, for example, in my case I am seqeuncing a clinical isolate of Klebsiella pneumoniae but I have no information about this bacterium and the most related species, Therefore, based on what do I choose a reference that is the most similar to my bacterium?
Thanks
I am not an expert on Klebsiella, but I suspect you can use BLAST against whole genomes in GenBank to identify other complete assembled genomes that are very similar to your contigs. There are dozens of Klebsiella genomes and some are well assembeled.
https://www.ncbi.nlm.nih.gov/nuccore/FO834906.1
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch
Here are a couple links to genomes that might help. I am not sure how many plasmids the typical strain carries in addition to its major chromosome. If there are a lot of plasmids it may be more difficult to assemble the genome.
https://www.ncbi.nlm.nih.gov/pubmed/?term=Klebsiella+pneumoniae+MGH+70
https://www.ncbi.nlm.nih.gov/nuccore/JMZF01000005
Hi Silvia
You could follow Brian's suggestions and after you could try CONTIGuator (http://contiguator.sourceforge.net/). It should be able to perform a blast-based scaffolding. It has been specifically developed to work with bacterial genomes.
Thank you to both of you. Is this tool (contiguator) supposed to work ? Because the URL, does not seem to work..do you other tools that allow to do the same thing?
Thanks
Hi Silvia
You are right, the Medusa link seems expired.
try the direct link to download: https://sourceforge.net/projects/contiguator/files/latest/download
Or try "http://contiguator.sourceforge.net/" and click on "Download latest version"
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