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sannazza 05-27-2020 07:02 PM

weird annotation, please help!
I've sequenced a bacterial genome using PacBio, de novo assembled it using three different assemblers (canu, flye and unicycler). They all worked more or less ok, and the assembled genome is around the expected size for the genus (around 7Gb). But when I try to annotate it, no matter if I use any of the three assemblies or two different programs (Prokka or RAST) I always get way too many more genes than other related species (9937 vs ca. 6500).
Any ideas of what could be happening? I'm really stuck here and can't figure out what is going on, so any help will be much appreciated!
Ana :confused:

GenoMax 05-28-2020 06:53 AM

Have you tried to use an assembly reconciliation tool? There may be a newer reference than this one of such tools.

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