Which sequencing platform should I consider for my project?

The table below shows the wide range of outputs from the sequencing platforms currently available in the Core. Illumina and PacBio offer very complementary technologies (Illumina: very high output, but shorter reads; PacBio: long reads at lower throughput). The choice of platform depends on the data requirements for your project – please contact us to discuss your options.

Sequencing Platforms HiSeq3000/4000 HiSeq2500 – Rapid Mode HiSeq2500 – High Output 1 MiSeq PacBio RS II
Sequencing Output per Lane average 104-110 Gb * up to 45 Gb up to 36 Gb 1 up to 15 Gb 500 Mb to 1 Gb  (official estimate after titration; potentially up to 1.2 Gb very dependent on library type, DNA quality, library titration)
Reads per Lane
in Millions (i.e. Clusters Passing Filter **)
average 340 -370 M * up to 170 M up to 200 M up to 17 M (v2)  up to 25 M (v3) 20-60 K
Read Length up to 2x 150bp up to 2x 250bp up to 2x 100bp up to 2x 300bp average 9-12kb, N50 up to 17kb
Typical Sequencing Format
SR (single reads), PE (paired end reads)
SR50, PE100, PE150 SR100, PE150, PE250 SR50, PE100 1 SR50, PE75 (v3), PE150, PE250, PE300 (v3) 1-3kb (CCS), 2kb, 5kb, 10kb, 20kb, 30kb

* The average yield for HiSeq 3000/4000 lanes and customer prepared libraries is 340 million clusters passing filter.  For libraries prepared by our facility the average yield is higher at about 370 million clusters.  The core-prepared libraries tend to show better size selection ( narrower fragment size range) and adhere closely to the recommendations for the Hiseq3000/4000 libraries and thus tend to cluster more efficiently than the average library.
** The number of “clusters passing filter” is equivalent to the number of “reads passing filter”  for single-end sequencing runs.  For paired-end sequencing the number of reads is twice the number of clusters according to the way Illumina is counting reads.
1 Due to the much higher read numbers enabled by the Hiseq 3000/4000 sequencers, we usually do not run the Hiseq 2500 in High Output mode anymore.  Please inquire with us if you would like to run entire flow-cells..

Category: 05 Sequencing

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