Genomics England, in partnership with the Sanger Institute, has been assessing the advantages of long-reads sequencing technologies over Illumina short-reads whole genome sequencing. The primary objective is to identify structural variants (SVs), repeats expansions and contractions, and epigenetic modifications that cannot be accurately detected with short-read sequencing.
The dataset consists of human genomes from a subset of 100,000 Genomes Project participants assembled with ultra-long reads. The genomic data deposited in the Research Environment were generated with the Oxford Nanopore Technologies (ONT) Promethion (Beta) and comprise the full output of the long-reads analytical pipeline 1.0.
This page includes information on the sequencing protocol, the analytical pipeline and a summary of the data within the research environment.
- Sequencing protocol
- Bioinformatics pipeline
- pipeline 1.0
- Files structure
Germline DNA from a subset of 100,000 Genome Project participants was depleted of low molecular weight DNA (<10 Kb) before library preparation. Libraries for ONT sequencing were prepared with the protocol indicated in the library_prep field of the ‘LRS_sample’ table in LabKey. Data were acquired with the PromethION Beta for 42-60hrs in high-accuracy mode. Full details of the protocol can be found here:
ONT pipeline 1.0
The ONT samples are structured as follows:
These files contain the raw output from the ONT sequencer in a HDF5 format. Each file contains the data for up to 4000 sequences.
This is the output of the ONT basecaller Guppy, containing the sequence and base-quality scores of each read.
The BAM file contains all pass filter reads and information on their alignment to GRCh38.
Structural variant calls against GRCh38 from the sniffles tool.