In vivo cloning such as AQUA or IVA offer the possibility to rapidly clone fragments of DNA into E.coli based on short sequence homology (15-40bp), so the cloning can be easily done in high throughput in competent strains such as JM109 or any cloning strain within a few hours.

But then for high protein expression, it would be more efficient to clone into BL21.

How can one obtain a high number of transformants by using in vivo cloning on BL21? The goal would be to directly be able to clone and express in less than a few hours.

For instance one could clone in vivo in BL21 and use antibiotic resistance as a positive selection such as what is explained in AQUA, then dilute the cloning culture in order to get at least 1 transformant by well in a 96 well plate containing IPTG, the protein would be expressed in 96 well plates and the readout would allow to screen for the best colonies.

Now according to previous finding from literature, BL21 has a low cloning efficiency by in vivo recombination, would it still be enough to generate at least 30-96 transformants ?

Of course it depends on the cell competency and on the amount of DNA used for cloning. But we wish to use as least as we can.

TLDR: Does anyone has any experience with in vivo cloning in BL21?