v2.1.0

In this release the summary scoring method for VDS has been updated to a weighted mean across residues in the Spike RBD only. This is designed to better reflect latest literature and observations of the newest Spike variants.

Full Changelog: v2.0.0...v2.1.0

v2.0.1

• Add pandemic scale baseline scores for comparison.
• Fix issue with single sample input processing.
• Update spike region calculation for scoring.

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

This version provides a major speedup to SPEAR (6mins for 1000 samples on a single core) and includes the following:

-Adds SPEAR utilities module, including utilities-report to run reports on past flat file outputs, and utilities-representative to produce representative VCF files for samples from the same Pango Lineage quickly (like those used in SPEAR-Reports repo).
-Utilises Seqkit to process input fasta files, necessitating a change in fa input. All samples should be combined into a single file, which can now be gzipped to reduce overhead.
-Similarly, VCF files can now be passed to the pipeline as a single multi-sample VCF file. A helped function, utilities-vcf-merge is provided to do this merging on a directory of VCF files.
-Fixes #45 by adding the force-single flag to bcftools merge in the pipeline.

Full Changelog: v1.1.3...v2.0.0

v1.1.3

Version 1.1.3

• Fixed installation issue related to bioconda grep
• Fixed issue related to empty feature counts tables in convert_format.py and summary reports.

Full Changelog: v1.1.2...v1.1.3

v1.1.2

Version 1.1.2

• Added new XBB variants to demo.
• Changed SPEAR demo baseline from BA.5 to BQ.1

Full Changelog: v1.1.1...v1.1.2

v1.1.1

Version 1.1.1

Renames fields from Barns to Barnes and tidies up some example VCF file names.

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's Changed in version 1.1.0

• New BA.1 and BA.2 comparison ACE2 scoring measures integrated.
• ACE2 scoring measure changed from sum to mean.
• Updated log handling in ACE2 scoring measures for mean calculation.
• Unified single and multi sample pipelines into single snakemake file.
• Streamlined file downloads needed on install/update by integrating more data into SPEAR.
• New BQ.1 and BQ.1.1 vcf files added.
• Default baseline BA.5

Full Changelog: v1.0.12...v1.1.0

v1.0.12

What's Changed

• Made per sample outputs an option, improving SPEAR execution time. Enable per sample outputs using the new flag --per_sample_outputs
• Added membrane protein annotation based on 7VGR/7VGS and Zhang et al. 2022 (https://doi.org/10.1038/s41467-022-32019-3)

Full Changelog: v1.0.11...v1.0.12

v1.0.11

Fixes issue in convert_format.py where incorrect dataframe grouping applied leading to error.

v1.0.10

Added new VCFs for emerging variants. Other minor bug fixes.