This app was mentioned in 2 comments, with an average of 1.00 upvote
The challenge here is that in Android only your DEFAULT SMS app can mark a message as read.
For MightyText, if you install the texting app SimplyText and make it the default app on your phone, then MightyText can communicate with SimplyText and mark the message as read.
There's a promising new SMS app from the makers of Mighty Text, called Simply Text.
It maybe needs a bit of work in terms of looks (and I really don't like the logo!) but the app is pretty solid and has some nice additional features like a button for pre-programmed quick messages ("I'm running late, be there in 5", etc) and a persitent notification which shows the 3 people you text the most and allows you to launch a new message to them with a single tap.
I was using it on a Moto G when QKSMS was struggling for reliability (think it was a RAM issue). Back on QKSMS now that I have my G3 back, but ST is a definite contender IMO.