v2.1.1

What's Changed

• added epitome_filter.py for removal of human seqs by @DOH-JDJ0303 in #19

Full Changelog: v2.1...v2.2

v2.1

What's Changed

• Dev 2.0 by @DOH-JDJ0303 in #17
• Dev v2.1 by @DOH-JDJ0303 in #18

Full Changelog: v2.0...v2.1

v2.0

Major overhaul of underlying clustering approach and reference creation process:

• New documentation page (still needs some love):
• All processes written in Python and use JSON and JSONL inputs / outputs.
• Segmented genomes are classified automatically using a distance-based approach. The most common segment name for each segment group is applied. This process is optimized using a global minhash per segment group rather than pairwise comparisons. This was developed to address misclassified segments or sequences with no segment assigned. Specifically, this fixes the misclassification of flu B segments 1 and 2 in NCBI.
• Clusters are created using a windowed approach, leading to greater discriminatory power for large genomes. This approach was developed to address the previous creation of a single Mpox reference genome, despite significant variability in the termini.
• Clusters are created using DBSCAN instead of hierarchal clustering of complete linkage. This greatly improves over partitioning of sequences. A similar process is now also applied during reference de-duplication (condensing).
• References can be optionally created using a "centroid" approach during clustering. This returns a real sequence that has not undergone any modification. Consensus generation has likewise been made optional.
• Consensus sequences are now created using numpy instead of awk.
• Metadata handling and summarization is greatly improved and simplified.
• References are output as single JSONL files containing both metadata and the reference sequence. This greatly simplifies downstream modification of reference sets, while also facilitating rapid processing and filtering by VAPER

Full Changelog: v1.5.5...v2.0

v1.5.5

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

v1.5.0

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.

v1.1.0

Major improvement to consensus generation.

v1.0.4

Changed from Docker Hub to ECR and increased default resources

v1.0.3

added ".gz" to make publish

v1.0.2

more condense issues

v1.0.1

condense only occurs when more than 1 reference