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I have an incoming project to which they would like us to perform metagenomic library prep and sequencing. They intend to give us gDNA environmental samples for library prep. They also wanted to see if it would be possible to sequence a set High-C libraries on the same flow cell (which I was able to determine is possible as long as the prepped library have same index size, run parameters, and I assign two set of libraries to their own lane).
I typically work on human samples, so this is a bit new to me.
After a bit a research I determined the library prep would follow normal DNA library prep methods, to which I would probably use NEBNext Ultra II FS DNA Library Prep with Sample Purification Beads to make the libraries.
However, my biggest challenge would be to determining sequencing kits size for the Novaseq 6000.
I typically do the following calculation to help me select a Novaseq kit for my runs:
(Number of samples) X (genome size) X (desired data output) = Total Gb
I know there is a sequencing kit calculator that Illumina has, but my biggest issue when determining the kit for this project is the genome size. When I look up microbial DNA size, I get a wide range of answers, and it is hard to pinpoint which one I should select for my kit determination.
Does anyone have any experience running shotgun metagenomic sequencing on a Novaseq 6000? Do you have any advice in relation to kit selection? Is there any additional advice you would give in conducting NGS metagenomic studies?
Any insight into this matter would be greatly appreciated.
I typically work on human samples, so this is a bit new to me.
After a bit a research I determined the library prep would follow normal DNA library prep methods, to which I would probably use NEBNext Ultra II FS DNA Library Prep with Sample Purification Beads to make the libraries.
However, my biggest challenge would be to determining sequencing kits size for the Novaseq 6000.
I typically do the following calculation to help me select a Novaseq kit for my runs:
(Number of samples) X (genome size) X (desired data output) = Total Gb
I know there is a sequencing kit calculator that Illumina has, but my biggest issue when determining the kit for this project is the genome size. When I look up microbial DNA size, I get a wide range of answers, and it is hard to pinpoint which one I should select for my kit determination.
Does anyone have any experience running shotgun metagenomic sequencing on a Novaseq 6000? Do you have any advice in relation to kit selection? Is there any additional advice you would give in conducting NGS metagenomic studies?
Any insight into this matter would be greatly appreciated.