Entering edit mode
2.2 years ago
ranatekan91
•
0
Hi everyone, I am new to this field. I am planning to do hybrid approach (PacBio+Illumina OR ONT+Illumina) for my study on gut microbiome. Could anyone please answer my naive question? Question is: How many long read sequencing (PacBio or ONT) would require per treatment for hybrid approach? For short reads, for example, maybe I will do sequencing of three replicate per treatment. Thank you.
It's hard to guess exactly what you mean, as you ask "how many sequences", but then it appears you mean how many samples given the example you give. I would also add how many treatments or samples you are targeting. And, if possible, the target sequencing depth you intend on taking as this can change the answers.
How many long read samples you need really depends on what you want to gain from them. If you just want to gain a good reference dataset with reads spanning your target locus, then you may only need one long read sample per treatment, which you can then map the illumina reads to. However, if the sample community is very complex and highly variable among samples, you might need to increase replicates or sequencing depth.
Another consideration is the number of available barcodes for multiplexing. Unsure about PacBio, but to my knowledge ONT offers 24 barcodes for their RNA cDNA library kits. No barcodes are available for direct RNA sequencing with ONT.