I am planning my PhD project and would like advise on the appropriate sequencing depth for understanding AMR genes and taxonomy from river water that is not considered to be heavily polluted, So that I can correctly calculate the batch size I can use with the Illumina NextSeq 2000 P3 cartridge which has 2.4B paired-end reads
Is the calculation below correct
2.4B Paired end reads / 2x80Million reads =15 Batch size
2.4B Paired end reads / 2x60Million reads =20 Batch size
2.4B Paired end reads / 2x50 Million reads =24 Batch size
I found the study below said ~80Million reads is needed for full AMR richness, would this be good practice for river water samples as well?
"effluent and pig caeca stabilized at a sequencing depth of ~ 80 million reads per sample (depth required to achieve 95% of estimated total richness, d0.95: 72–127 million reads per sample)."
Gweon, H.S., Shaw, L.P., Swann, J. et al. The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome 14, 7 (2019). https://doi.org/10.1186/s40793-019-0347-1
- Badges
- Science topic