We utilize the amplicon generation process as our primary entry quality control. While our PCR conditions are optimized, the success of amplicon generation heavily depends on the amount of bacterial, archaeal, or fungal DNA present in the sample.
DNA Extraction Quality: If we extract the DNA, the quantity of extracted DNA is evaluated using spectrophotometry.
Initial Assessment: If we are unable to generate an amplicon or if the generated amplicon is very weak, it serves as a strong indication that the DNA content may be insufficient.
Negative Controls: Each batch includes negative controls (sterile water) to detect any potential contamination during sample preparation.
Sequencing Quality Assessment:
- Read Quality Monitoring: After sequencing, the quality of the reads is assessed using metrics like Q-scores. This helps identify any potential issues with sequencing accuracy.
- Filtering of Low-Quality Reads: Low-quality reads and adapter sequences are removed during the bioinformatics analysis to enhance data quality.