What's Changed

• Dev by @DOH-JDJ0303 in #12
• Bump dawidd6/action-download-artifact from 2 to 6 in /.github/workflows by @dependabot in #11

New Contributors

• @dependabot made their first contribution in #11

Full Changelog: v1.5.0...v1.5.5

Major changes to how input handling, metadata wrangling, and clustering.

Input handling:

• EPITOME will now automatically download all complete sequences and associated metadata, unless told not to.
• Input QC is now handled in R, rather than Bash to aid metadata capture on the backend

Clustering:

• Switched from Mash to Sourmash for better ANI prediction

Metadata:

• Sequence metadata is now summarized for each reference. This can be used for things like predicting sample taxonomy or host based on the reference genome metadata.

Major improvement to consensus generation.

Changed from Docker Hub to ECR and increased default resources