I am trying to assemble the whole genome of a metagenome-assembled genome. For this purpose, I am trying to plot a rarefaction curve which will tell me if I need to do any deep sequencing so that more information can be obtained. Can you provide a step-by-step guide on how to do that? For diversity, I know that I should plot 16S/18S on the y-axis and no. of reads/sequences on the x-axis, but I don't know what takes on the y-axis in case of whole-genome assembly.
Dear Adarsh,
It is not exactly rarefaction curve, rather collector's plot, but you could try to assess your coverage via genes. Then, plot number of genes obtained against number of reads.
Best regards,
Marcin Golebiewski
I think this paper would help you a lot https://genome.cshlp.org/content/30/3/315.full
" assemble the whole genome of a metagenome-assembled genome "
>> Do you want to assemble a MAG from raw data or you want to curate a MAG? It is not clear in your question. Both of previous answers are worth considering.
Additionally, rarefaction is not a much-used method nowadays as it has many limitations. Moreover, a single marker gene also is not very useful. 16S sequences are mostly not covered in the MAG assembly because they have a tendency to be binned in a few bins instead of all the bins recovered from raw data. This is due to the highly conserved nature of 16S genes. That is the reason, COGs are preferably used and not a single marker.
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