Please find below some of the details related to the study:
1. Total no of samples: 640
2. Organism genome size: 500 mb (in related species)
3. Restriction enzyme pair: SbfI and MSpI
4. Size selection fragments: 250-600 bp
5. Platform for sequencing: NovaSeq PE150 (120 G raw data per sample)
6. Multiplexing: 48 adapters X 12 PCR index
Looking forward to getting some help here
To estimate the number of samples that should be pooled in an individual library if 30X coverage is desired in a DDrad seq experiment, you need to consider several factors, including the total number of samples, the organism genome size, the restriction enzyme pair, and the size selection fragments.
Assuming that you want to achieve a total of 30X coverage across all 640 samples, you would need to generate a total of 19.2 terabases (640 samples x 30X coverage x 500 Mb genome size). Given that you have 120 Gb of raw data per sample on a NovaSeq PE150 platform, you can calculate the number of samples that can be pooled in an individual library using the following equation:
Number of samples per library = Total amount of data per library / (Desired coverage x Genome size)
Assuming a 10% loss of data during sequencing and data processing, you can use 108 Gb (120 Gb x 0.9) of raw data per sample. Using the above equation, you can calculate the number of samples that can be pooled in an individual library as:
Number of samples per library = 108 Gb / (30X x 500 Mb) = 720
Therefore, you can pool up to 720 samples in an individual library to achieve 30X coverage across all samples. Since you have 48 adapters and 12 PCR indexes, you can divide the 640 samples into 14 libraries (720 samples per library) for multiplexing, allowing for some extra capacity in case of suboptimal sequencing.
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