I’m trying to figure out how many samples per run I can sequence on various platforms for shot-gun metagenome sequencing.
I’ve read that 100-150 Gbytes per sample are recommended for WGS of human genomes, which is up to 12 samples per run on HiSeq 4000. Or 100-150 Gbp assuming that 1 bp + quality data = 1 byte.
I wonder what recommendations are for shotgun sequencing (and 16S) metagenome sequencing. I haven’t found any specifically for metagenome sequencing except at https://microbiomeinsights.com/shotgun-metagenome-analysis/ where at least 16(giga?)base pairs are recommended for "shallow sequencing which provides basic taxonomic functional profiling".
Hello Maxim,
One way to think about this is to ask how complex the microbial community is, and how interested are you in the rarer members? If the community is dominated by a few organisms, and you are mostly interested in the changing balance between them, then you don't need to go so deep. If the community is very complex, or you are interesed in very rare members, then you need to go deeper.
Gut bacteria analysis may be very different from soil, for instance, because of the difference in the complexity of the communities.
You could start by looking for recent papers which describe experiments with samples that are roughly similar to yours, and looking how deep they went.
Hello Maxim,
I would say for a basic characterization you would need at least 10gbp of data per sample, but the deeper you go, the more characterization of low abundance members of the sample you will have. Please take a look at the https://www.nature.com/articles/nbt.3935 publication. I hope it's useful!
Kind regards,
Hello Maxim,
One way to think about this is to ask how complex the microbial community is, and how interested are you in the rarer members? If the community is dominated by a few organisms, and you are mostly interested in the changing balance between them, then you don't need to go so deep. If the community is very complex, or you are interesed in very rare members, then you need to go deeper.
Gut bacteria analysis may be very different from soil, for instance, because of the difference in the complexity of the communities.
You could start by looking for recent papers which describe experiments with samples that are roughly similar to yours, and looking how deep they went.
Hi Maxim,
As suggested by Jonathan data in bytes/bp is depends on how complex microbial community. Requirement of data is differ from sample to sample.
- Badges
- Science method