New in Solu: reference-based phylogenetics, file downloads

Do not index

Reference-based phylogenetic pipeline

After extensive validation, we have updated Solu's phylogenetic pipeline with an important change. We've changed the tree calculation from neighbor-joined pairwise SNP distances to the following reference-based approach:

Quality correction of low-quality reads with fastp

Variant calling for each sample against a reference genome using snippy

Generating a multi-genome alignment using snippy-core

Filtering out low-quality SNPs

Calculating a phylogenetic tree with a maximum-likelihood approach using IQ-TREE

Midpoint-rooting the tree with Augur

All of this happens automatically, finishes within minutes, and requires no coding or configuration.

Reference-based phylogenetics is available for the following species: A.baumannii, A.pittii, C.auris, E.cloacae, E.coli, E.faecium, E.hormachei, K.pneumoniae, K.quasipneumoniae, M.abscessus, P.aeruginosa, S.aureus, S.enterica, S.epidermidis, and S.pneumoniae.

The upgrade will improve the tree's accuracy for datasets with high genetic variance. We've also improved the scaling of very large and small trees.

File downloads

You can download assembled genomes directly from the platform.

Use Solu as a fast way to de novo assemble and export genomes

Useful for follow-up analyses (e.g. BLASTing or visualization with tools like JBrowse)

We plan to include other files in this menu as well, such as the raw outputs of SNP calling and other tools in the pipeline. Let us know what files you'd want to download!

Other updates

You can now select multiple rows to download or delete multiple samples at once

Small-screen usability has been improved. You can now toggle the sidebar on and off

The performance of large workspaces has been improved

Multiple small bug fixes and performance improvements