Hi

Our lab has just received a 5500xl upgrade for our SOLiD 4 and I have some newbie questions that I haven't found answers for in our 5500 documentation.

1. Can we re-run libraries, i.e. a set of exome sequence captures, which were prepared for the SOLiD 4 on the 5500. I know that 5500 libraries have a new A-tailing step, but does this affect the sequencing? We would make fresh bead preps using our EZ-Bead system.

2. How many beads need to be deposited per lane? How many are actually sequenced? If we switch to nanobeads, how much improvement will there be?

3. How many panels are there in each lane? How many are imaged? I've seen three different numbers mentioned: 670 panels/lane is assumed in the reagent cost calculator; 708 panels/lane was provided by my FAS; and 1200 panels/lane are mentioned in the user guide (when calculating the number of beads to be deposited, i.e. 1200 panels x 250k beads/panel). I want to estimate how much sequence will be produced from each lane.

4. How long do sequencing runs take on the 5500xl? I know that they can do different types of runs at the same time, but assume all 12 lanes (2 flowchips) are either all single 75 bp reads or all 75+35 bp PE reads for simplicity. I want to estimate how many runs a year we can perform.

Finally, how well have these new machines been working for everyone? We're looking forward to all the promised improvements.

Thanks everyone

Our lab has just received a 5500xl upgrade for our SOLiD 4 and I have some newbie questions that I haven't found answers for in our 5500 documentation.

1. Can we re-run libraries, i.e. a set of exome sequence captures, which were prepared for the SOLiD 4 on the 5500. I know that 5500 libraries have a new A-tailing step, but does this affect the sequencing? We would make fresh bead preps using our EZ-Bead system.

2. How many beads need to be deposited per lane? How many are actually sequenced? If we switch to nanobeads, how much improvement will there be?

3. How many panels are there in each lane? How many are imaged? I've seen three different numbers mentioned: 670 panels/lane is assumed in the reagent cost calculator; 708 panels/lane was provided by my FAS; and 1200 panels/lane are mentioned in the user guide (when calculating the number of beads to be deposited, i.e. 1200 panels x 250k beads/panel). I want to estimate how much sequence will be produced from each lane.

4. How long do sequencing runs take on the 5500xl? I know that they can do different types of runs at the same time, but assume all 12 lanes (2 flowchips) are either all single 75 bp reads or all 75+35 bp PE reads for simplicity. I want to estimate how many runs a year we can perform.

Finally, how well have these new machines been working for everyone? We're looking forward to all the promised improvements.

Thanks everyone

## Comment