COVID-19 long read sequencing¶
We sequenced a subset of the Covid-19 cohort using Oxford Nanopore technology (ONT).
We have a total of 191 participants with ONT data, split in the following way:
- 99 Covid-19 mild participants
- 92 Covid-19 severe participants
The data are found in s3 buckets accessible from CloudOS located under
GEL genomes > covid-19 > oxford_nanopore. The table
linking_table_covid_ont.tsv provides the file paths to the data and a link to the
For each participant we make available:
- BAM file
- Structural variant VCF
- HLA genotyping files
Basecalling was performed with guppy version 4.0.11+f1071ce using the high accuracy model.
A brief description of the analysis workflow:
- Reads with an average base quality score >= 7 were merged with FastQC.
- Reads were aligned to GRCh38 with minimap v2.10-r761 (parameters: --secondary=no -x map-ont --MD).
- NanoPlot v1.32.1 was used to produce QC reports on basecall sequencing summary and aligned reads.
- Aligned read coverage was assessed with mosdepth v0.2.6.
- Structural variants were called with Sniffles v1.0.11 with the following parameters: --min_support 3 --minmapping_qual 20 --min_seq_size 1000 --report_read_strands --genotype --cluster.
- HLA genotyping was conducted with HLA-LA v1.01.