I have been using a standard hot-start Taq polymerase for processing samples for NGS.
My samples are low yield so when working with them before NGS preparation, this mix with the standard hot-start Taq was the only Taq that would consistently amplify from all of the samples to a level that would enable further analysis. Hence, I have continued using it on the basis that getting the good amplification to sequence in the first place outweighs any additional error that might arise from not using a proof-reading Taq.
I was thinking of going to the supplier for the standard Taq I now use and seeing if they do a high-fidelity version of the same Taq. I was just looking for further opinions on this before I start my sample preparation?
Thanks
Personally not encourage non-proof reading Taq for NGS. NGS provides very high coverage. You can try using Q5 high fidelity Taq Polymerase (NEB), with >100X fidelity than normal Taq.
What Taq are you using?
I haven't tried any Taq that doesn't have proof reading ability for NGS and I'd shy away from it. What does your data look like? Do you lose a lot of reads or have odd allelic ratios? I have cloned using a "low fidelity" Taq that amplified well spiked in with pfu turbo and that helped with fidelity, but I'm not sure if this would be optimal for NGS for library enrichment due to the processivity of pfu. If you're looking for somatic mutations, you'll need the best fidelity taq you can find.
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