Long-read genomic data

Genomics England, in partnership with the Sanger Institute and Pacific Biosciences amongst others, has been assessing the advantages of long-reads sequencing technologies over Illumina short-reads whole genome sequencing. To this end, we have employed both Oxford Nanopore Technologies and Pacific Biosciences methodologies.

Upon availability of the data and/or expiration of potential embargoes we aim to provide researchers access to this data.

A separate section has been made available in LabKey as of 100kGP Data Release v17 containing various tables related to long read sequencing data.

Datasets available

Dataset	Technology	Project	Type	Summary	Participant count	Data types	Data location	Tables
ONT rare disease pilot	Oxford Nanopore	100kGP	Rare disease	First ONT data set with structural variant calls	315	Regular BAMs Structural variants	/gel_data_resources/LRS_cohort_genomes/Rare_Disease/	LabKey rare_disease_ont_cohorts
ONT cancer pilot	Oxford Nanopore	100kGP	Cancer	First ONT data set generated for 100kGP cancer participants and first data set with methylation calls	100	Regular BAMs Methyl BAMs	/gel_data_resources/LRS_cohort_genomes/cohort_CML	LabKey cancer_ont_cohorts
PacBio rare disease pilot	PacBio	100kGP	Rare disease	Example dataset to demonstrate the utility of PacBio's HiFi technology	91	Small variants Structural variants	/gel_data_resources/LRS_genomes/WGS_PacBio	LabKey rare_disease_pacbio_pilot
ONT pilot	Oxford Nanopore	100kGP	Rare disease	First ONT data set generated for 100kGP participants	47	Raw sequencing data (FAST5) FASTQ Regular BAMs	/gel_data_resources/LRS_genomes/WGS_ONT/	LabKey lrs_laboratory_sample and lrs_sequencing_data
ONT COVID-19	Oxford Nanopore	COVID-19		Mild and severely affected COVID-19 participants	191	Structural variants HLA genotyping	CloudOS GEL genomes > covid-19 > oxford_nanopore	linking_table_covid_ont.tsv