HiSeq 4000 PacBio Sequel Proton
HiSeq 2500


The High Throughput Sequencing Facility has 2500 sq. ft. of dedicated wet bench lab space housed in a new 9000 sq ft. facility along with the UNC gene expression core. The HTSF has Illumina HiSeq 2000, 2500 and two 4000 instruments, as well as two Illumina Genome Analyzer II machines, an Ion Proton Sequencer, and a PacBio RS II (SMRT) sequencing system, and associated equipment necessary for efficient operation.

All sequencers are associated with on board computers for real-time data processing, with three servers dedicated for data analysis and distribution. Sequencing data processing, management, initial analysis, and distribution of all data generated at the HTSF are handled by the UNC Center for Bioinformatics, which is responsible for application support, training and consultation for bioinformatics needs for researchers.

MiSeq HiSeq Ion Proton PacBio
Key applications Small genome, amplicon, and targeted gene panel sequencing, confirming complex balanced pools Production-scale genome, exome, transcriptome, sequencing, and more Production-scale genome, exome, transcriptome, sequencing, and more The same as HiSEQ with longer read lengths and more reads Small genomes, targeted sequencing, exome and transcriptome sequencing, low complexity samples Whole genomes, transcriptomes, complex populations, epigenetics, structural variants
Platform MISEQ HiSeq 2500 HiSeq 2500 HiSEQ 4000 P1 318 Sequel
Nickname for system n/a Rapid Run V4 or High Output n/a n/a n/a n/a
Flowcells processed 1 1 or 2 1 or 2 1 or 2 1 chip 1 chip 1 SMRT cell
Depth 0.3 – 15 Gb 50 – 60 Gb (2x100bp) 450 – 500 Gb (2x125bp) 650-750 Gb (2x150bp) 10-15 Gb (1x200bp) 1 Gb (1x400bp) 750 Mb – 1.25 Gb
Run time 5 – 65 h 1 dy – 2 dy 1 dy – 7 dy 1 dy – 3.5 dy 4 hr 6 hr 6 hr
Lanes/flowcell 1 2 8 8 1 1 1
Max PE Reads/flowcell 25 million 300 million 2 bilion 2.5 billion 80 million 6 million 370,000
Read Type Format Single or Paired End Single or Paired End Single or Paired End Single or Paired End Single End Single End n/a
Read Length Available 50X, 100X, 150X, 250X, 300x 50X, 100X,150x,250x 50X, 100X,125x 50x, 75x, 100x, 150x 50-200x 50-400x >20 Kb
Guaranteed read #/lane (see note below) 15M , single end, New Chemistry 100M, single end 130M, single end 200M, single end 75M single end 4M single end
30 M, Paired end, New Chemistry
8 M, single end, Old Chemistry 200M, paired end 260M, paired end 400-450M, paired end n/a n/a n/a
16 M , paired end , Old Chemistry
Read Number Guarantee : The number of reads is only guaranteed for standardized libraries prepared and pooled by the HTSF. For novel library preparations, the HTSF may require a pilot to determine if we are capable to meet the goals. The pilot will typically be at the expense of the project. We can not guarantee the length for libraries and / or pools prepared by studies. We will make every effort to have successful seq results. But the number of reads per library , especially in the case of novel library preps or unbalanced pools may not meet the read per lane goals. Keep in mind that the above table refers to high diversity genomic DNA samples. For most other applications a 10% reduction in yield is to be expected.