Dear all,
Another shot at Illumina as the Gold Standard, now for variant calling:
Hall MB, Wick RR, Judd LM, Nguyen AN, Steinig EJ, Xie O, et al. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. In: eLife [Internet]. eLife Sciences Publications Limited; 10 Oct 2024 [cited 22 Jan 2025]. doi:10.7554/eLife.98300 https://elifesciences.org/articles/98300
From the abstract: "We also investigated the impact of read depth on variant calling, demonstrating that 10× depth of ONT super-accuracy data can achieve precision and recall comparable to, or better than, full-depth Illumina sequencing. These results underscore the potential of ONT sequencing, combined with advanced variant calling algorithms, to replace traditional short-read sequencing methods in bacterial genomics, particularly in resource-limited settings."
The authors attribute the higher recall scores of ONT variant calls (counter-intuitive given their lower average base Q-score, even if the gap with Illumina is closing) to better resolution in variant-dense and repeat regions.
Cheers Marco