What challenges would assembling a draft genome with non-cultured isolated eukaryotes pose? Through individual cell picking, centrifugation, and membrane filtration we hope to isolate eukaryotic single-celled organisms. However, it is likely that these isolates will also contain other microorganisms, that while interesting, are not our main focus. So, how difficult will it be to distinguish sequences from our organism of interest from others in the sample during genome assembly and alignment? Is this mostly dependent on the resolution of the reference database?
Kevin Amses at the University of Michigan has been working on this problem, and has a very good pipeline: https://github.com/amsesk/scgid
I highly reccommend it, and he is fairly good at answering questions about how it works and troubleshooting hiccups. We used a draft version of his pipeline to assemble our genomes (Article Genome-scale phylogenetics reveals a monophyletic Zoopagales...
)The difficulty will be correlated to the phylogenetic relatedness of the taxa. For example, it will be harder to separate two fungal species in the same genus from each other than to separate a fungal species from a euglenoid, for example.
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