The choice of the appropriate sequencing device depends on the targeted data amount. The benefit for you is that we can offer you the right sequencer with the optimal balance of data output, time and costs as actually one HiSeq 2500 and two MiSeqs are available at the NGS Core Facility.
Illumina´s HiSeq 2500 system is characterized by its flexible run configurations which can be adjusted with regard to data output or time. On the other hand, this sequencer is the appropriate device for high-throughput experiments like whole-genome, exome or whole transcriptome sequencing. By using the latest sequencing by synthesis (SBS) chemistry (v4), one flowcell can generate within 6 days up to 500 giga bases (Gb) with 2×125 basepairs (bp) read length or up to 4 billion paired-end reads. This is equivalent to sequence about 96 human transcriptomes or 64 human exomes at appropriate depth. For expression analyses, 200 samples can be analysed via 3´-mRNA sequencing with this flowcell (generating 10 million reads per sample). On the other hand, it is also possible to perform experiments in a so called rapid run mode. Here, one flowcell generates up to 150 Gb with 2×250 bp read length or up to 600 million paired-end reads within 60 hours.
The MiSeq sequencer is Illumina´s benchtop solution for small-sized sequencing projects. It is suitable for a broad range of applications like targeted gene sequencing, metagenomics (16S rRNA), amplicon sequencing (i.e. of CRISPR-Cas9 mutated clones), small genome sequencing, targeted gene expression, and HLA typing. Using the latest version of reagents (v3), up to 15 Gb of output can be generated (with 50 million paired-end reads and 2×300 bp read lengths). For smaller projects, a scale-down regarding output and costs is also possible with the previous version of reagents (v2). Therefore, it is possible to adjust the approach according to your needs regarding data output and budget.
Due to diverse research topics there are numerous specific protocols for sample preparation available. Therefore, our customers are asked to prepare samples and libraries by themselves. For quality control and library preparation you can use our TapeStation 2200 (Agilent), Qubit and Quant-iT (Thermo Fisher Scientific), Bioruptor pico (Diagenode) and SPRI-beads based purification systems.
NGS generates a huge amount of data which require bioinformatics solutions. At the NGS Core Facility, we provide customers with access to different software tools, such as the CLC Biomedical Genomics Workbench and Server (Qiagen) or Cartagenia’s Bench lab NGS (Agilent), to perform their bioinformatics analyses. More complex statistical analyses can be addressed in cooperation with the Bioinformatics Core Facility or with the Institute of Medial Biometry, Informatics and Epidemiology (IMBIE).