From: The effect of DNA extraction methodology on gut microbiota research applications
Methods | Pros | Cons |
---|---|---|
Chaotropic (CHAO) | Highest DNA yield | Most fractional loss of reads after different steps of bioinformatics pipeline |
High coverage in sequencing | Takes longest to perform | |
Lowest loss of read trimming | ||
Cheap | ||
Phenol Chloroform (PHEC) | Cheap | In the middle in terms of performance compared with the other methods |
Highest dsDNA in probiotic sample | Use toxic reagents | |
Quicker than CHAO | ||
QIAamp DNA stool minikit (QIAG) | Highest read yield post OTUs assignment | Lowest DNA yield |
Quick | Not cheap | |
Highest quality DNA | Lowest coverage | |
Can be automated |