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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 participant_id.

For each participant you can see:

  • BAM file
  • Structural variant VCF
  • HLA genotyping files

Data generation

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.