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biocore / emp

Code repository of the Earth Microbiome Project.
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16 EMP - Adaptor timming #130

Open fconstancias opened 1 year ago

fconstancias commented 1 year ago

Dear EMP protocol users,

We are using the EMP protocol (515F - 806R, forward-barcoded) to generate 16S libraries.

I am not sure which sequence/tool should I use for adaptor trimming when using the protocol. Do you have any recommendation?

Thanks

justinshaffer commented 1 year ago

Hello,

We recommend using QIIME 2's demux plugin's emp-paired or emp-single method, depending on whether your sequence data are paired or not.

https://docs.qiime2.org/2022.11/plugins/available/demux/

This approach will demultiplex your reads and trim primers and adapter sequences, but only works for data generated using the EMP protocol as you are. If other library construction methods are used we recommend using QIIME 2's cutadapt plugin for removing adapter and primer sequences.

Best wishes,

Justin

On Wed, Jan 18, 2023 at 12:48 AM Florentin Constancias < @.***> wrote:

Dear EMP protocol users,

We are using the EMP protocol (515F - 806R, forward-barcoded) to generate 16S libraries.

I am not sure which sequence/tool should I use for adaptor trimming when using the protocol. Do you have any recommendation?

Thanks

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