Here is the link to the preprint:

www.biorxiv.org/content/10.6...

Give it a try and let us know what you think. As with any project, any feedback/thoughts from the community are well appreciated! Written in Rust :)
github.com/treangenlab/...

6/n

For samples that are aligned to a single reference, bronko can also generate a multiple sequence alignment, which can be directly input into downstream phylogenetic/transmission inference tools. We found that the SNPs identified matched well with Parsnp2 in cases of low divergence.

5/n

bronko also take multiple samples and multiple references, mapping each sample against all of the references at once. This allows us to choose the reference that most closely matches the reference genome, reducing biases that can arise from distant references

4/n

To achieve this, we utilized a (1,2) locality-sensitive bucketing function, which matches kmers with <= 1 edit distance from the reference and precisely identifies SNPs/iSNVs within those kmers. Combined with a pseudomapping approach, we can identify most variants directly from k-mer counts.

3/n

We developed bronko, an alignment-free approach that bypasses both read-alignment + variant calling and provides variant calls (SNPs and iSNVs) directly from sequencing reads and a reference genome (or set of reference genomes), enabling viral genome analyses across petabyte-scale databases

2/n