We base our recommendations on empirical evidence and industry best practices to ensure a minimum number of high-quality microbial reads. The goal is to retain enough usable data after removing host reads to support robust taxonomic and functional profiling.
| Host DNA Contamination |
Example Environments |
Recommended Read Pairs |
Why? |
| < 25% |
Stool, Tongue |
10 million |
Low host DNA → most reads are microbial. 10M pairs usually provide sufficient microbial diversity and coverage. |
| 25–60% |
Skin |
30 million |
Moderate host DNA → 40–75% of reads may be host. More reads are needed to retain a comparable number of microbial reads. |
| > 60% |
Saliva, Nostrils |
50 million |
High host DNA → >60% of reads may be discarded. Higher sequencing depth ensures enough microbial reads remain for analysis. |