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Old 01-08-2019, 08:08 PM   #6
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Location: Eugene, OR

Join Date: May 2013
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I think the confusion is that they are calling all the contigs except for the largest "plasmid" which would be premature to do so without other evidence, especially if they are called as non-circular. Other than that, it is an OK PacBio assembly. I'd say a majority of the time a bacterial genome assembles as a single contig but a significant minority is fragmented into multiple contigs.

I'd blast the resulting contigs. Usually it is obvious if it is a plasmid from the blast results. If you really really want a better assembly then it might be worth to re-sequence now that newer kits have been released with longer read lengths. The short fragment size may have been due to DNA quality, though.

I would try Canu assembly with a higher expected coverage since you have the read depth to do so. The only other thing I can think of is that some libraries have high rates of palindromic reads due to un-repaired ends folding back and acting as a barbell adapter. This can mess up assembly. The newest version of the SMRT assembler chooses a single subread from each well to avoid some of the problems with the palindromes (I think) so I'd check if they assembled with the System 6 update. We filter palindromes before Canu to avoid the problem.
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