PacBio Upgrade

The PacBio was recently upgraded to version 1.3.3. With this upgrade comes the ability to use the XL versions of the DNA/Polymerase Binding and DNA Sequencing kits. These new kits should result in a longer average readlength (5000 bp) in comparison to the ~3000 bp average we get with the current C2 chemistry.

Using both new kits together does come at a cost. The data produced with the DNA Sequencing Kit XL 1.0 will be of a lower quality than with C2, and is recommended only when the data will be error corrected with shorter, more accurate reads.

For a boost in average read length without sacrificing quality of the reads, the DNA/Polymerase Binding Kit XL 1.0 can be used with the C2 sequencing chemistry rather than with the newer XL sequencing kit.

More details to follow…

MiSeq: More reads and longer read lengths are now available

Over the past couple of months we have been evaluating the MiSeq upgrade. This upgrade includes the ability to sequence longer reads (250nt from each end, so 500 nt per library fragment) and to collect data from more clusters (both the top and bottom of each channel are imaged). We just had a 250 PE run that exceeded 30 million reads – that is just over 8 Gbases of data! This is a nice jump up from the ~13M reads (~2 Gbases) per run we were getting before.

Disclaimer: We are still in data-gathering mode to determine what the average expectation should be for each run- it would be nice to get 30 million reads from every run, but that may not happen.

Here are quality plots of a 250 PE run with genomic PE libraries. We are working to maximize quality as the read lengths increase.

Read 1:

Read 2:

We can now combine the benefits of Illumina’s high read counts with the benefits of longer reads.

Up next is to see how MiSeq/Pac Bio hybrid assemblies measure up to HiSeq/454 hybrid assemblies, and a comparison of assemblies using HiSeq 100bp PE reads vs MiSeq 250 bp PE reads.