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Table 1 Summary of findings reported in this study

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