Sample handling and shipping
Because DNA extraction is often the primary source of bias in microbiome workflows, we carefully optimized and fully automated this step. Poor lysis can result in underrepresentation of DNA from gram positive and other difficult to lyse organisms. On the other hand, overly aggressive lysis can lead to DNA degradation. Finally, stool contains many inhibitors that can interfere with downstream enzymatic reactions. With these parameters in mind, we developed a robust process for reproducible extraction of inhibitor-free, high molecular weight genomic DNA that captures the true microbial diversity of stool samples.
After DNA extraction and QC, genomic DNA is ready to be converted into sequencing libraries. This library preparation process can also be a significant source of bias in metagenomics analysis. Thus, we selected a library prep method with minimal GC bias. We also use unique dual indexed (UDI) adapters to ensure reads and/or organisms are not misassigned to the wrong sample due to index hopping.
Shotgun whole genome sequencing
Sequencing data is automatically uploaded to One Codex and analyzed against our One Codex Database, consisting of more than 115k whole microbial reference genomes. A rapid, highly sensitive k-mer classification algorithm maps sequencing reads back to the reference genomes.
The raw classification results are filtered through several statistical post-processing steps designed to eliminate false positive results caused by contamination or sequencing artifacts. The One Codex analysis provides a detailed, highly accurate picture of the composition of your samples, giving you complete confidence in your results.