Mixing amplicon and (meta)genomic libraries on one sequencing chip?

[Mabeuf]

I was told many a year ago that you couldn't combine amplicon seq and meta/genomic seq libraries into one pool because of something to do with the monogenic nature of the amplicons.

However I can't find any evidence of this online when trying to explain this to someone else, and some people seem to have done it on this forum.

Does anyone have any experience of this? Thanks!

(Particularly we're using an illumina machine)

[nucacidhunter]

Pooling one amplicon library with a high diversity library or any other amplicon is better than not pooling because that will increase sequence diversity of an amplicon library making higher clustering and increased sequencing yield possible.

[thermophile]

Yup we pool genomes and amplicons all the time, saves us from having to run so much PhiX