Sequencing on the PromethION

We use the latest R10.4.1 flow cells and Kit 114 library to ensure the highest accuracy. To preserve DNA methylation, we use the 'native ligation' module which sequences the genomic DNA without any amplification. For multiplex we use the native ligation barcoding kit. 

Base calling: Guppy or Dorado

Base calling converts the raw signal into bases and calls DNA methylation at cytosines. We use Guppy or the newer Dorado base caller with the latest neural network models from ONT to call your bases at 'super accuracy' mode.

Quality Control

Each run comes with a QC file in html format with metrics for read lengths, PHred score, and flow cell performance over time. The file is interactive.

Alignment and Coverage Statistics

All reads are aligned to the genome of your choice during base calling if you request. The output file is in bam format and will contain all aligned and unaligned reads, ready for downstream processing. Depth will be provided with alignment.

Global DNA Methylation

Standard sequencing service comes with global methylation values for both 5mC and 5hmC (when selected as an option)

Files delivered

The standard file delivered is the BAM file containing all aligned and unaligned reads. This is a 'modified' bam file containing all modified DNA marks by the base caller. This file can be directly converted into FastQ either by us or by you. We also deliver the methods in a text file consisting of the software versions and descriptions of all parameters used in the generation of these files.