Miseq, long reads vs short reads

Hi there

I did Miseq to some samples a couple of months ago in a company where they sequenced the V4 region of my samples and I ended up with reads of 250bp
I did the analysis (with a lot of help from this forum, thanks for that) and I was pretty happy with it even if I didnt have that long reads!

It seems however that I cant continue sending my samples to that company and I have to find a new one, which I did
In that new company that I found they say that they use 2 protocols: one that amplifies the V1-V3 region and one that amplifies the V3-V5 region and that the reads they produce are about 570bp!!!
from what I understood (and what they told me) is that they create a longer amplicon and when they assemble afterwards the reads there is only a small overlap

i m a bit reluctant to use a protocol like that but I would also like to hear other people’s opinion
do you think its a good idea? should I go for it? or should I just stick to the protocol with the shorter reads (and better overlap)


I would not do either option. The 300PE kit is not ready for 16S rRNA gene sequencing. The quality in the second read really falls off. If you would like to email me, I can get you in touch with a core here at Michigan that would be happy to perform the Kozich et al. method for you.


thanks! I ll see what other options we have and I might contact you!