In general Illumina sequencing read size is about 75-150, sometimes 200, depending on library preparation protocol. Some kits claim sequencing up to 300 bp per read, however, as practise shows, such long reads inevitably have significant quality loss after 200 bp.

Considering your task, use of MiSeq is an overkill. Sanger sequencing with capillary machine works fine with fragments shorter than 1000 bp, and it is much easier to prepare and less expensive.

Dear Dr. Alexandr Pozharskiy, thank you so much for your wise suggestions.

150-250bp

You can sequence on MiSeq but you will not be getting any overlap so, no merging will be possible for the read-pairs.

But if you have metagenomics sample, Sanger sequencing is not a direct option. For that you have to go for clone library prep.

Here you have a trade-off. Either go can go for high-throughput or high-accuracy.

But both will have its own down-falls. High-throughput will not give you longer length (good enough accuracy), but sanger will have low-throughput and accuracy would depend on how the cloning and sequencing worked.

You just have few (20-30 bp) extra in your amplicon, otherwise if the amplicon length was aroung 570-580 bp, it was okey for MiSeq paired-End.okayaround.

We have a very similar problem for our marker gene but in our case, MiSeq was good enough. Follow my updates, the paper with different comparison scenario is coming soon.