v2.0.4

What's Changed

• rename smitis sequence by @Oliver-Lorenz-dev in #23
• remove 0 from 34 by @Oliver-Lorenz-dev in #24

Minor nomenclature changes only

Full Changelog: v2.0.3...v2.0.4

v2.0.3

What's Changed

• rename to NCC convention by @Oliver-Lorenz-dev in #20
• Add 33f subtypes and bug fixes by @Oliver-Lorenz-dev in #21

Add in subtypes for 33F:

• 33F-1a - GPS_US_PATH3618
• 33F-1b - MK606435

Minor fixes for 20A and 33H to output detailed output file.

Full Changelog: v2.0.2...v2.0.3

v2.0.2

What's Changed

• Update non encapsulated references by @Oliver-Lorenz-dev in #19

Update non encapsulated references to include newer sequences and rename already present sequences to something more descriptive.

• Rename Swiss_NT to Group3_aliC_aliD_non_encapsulated (NCBI accession - HE651292)
• Rename alternative_aliB_NT to S_mitis_Group3_aliC_aliD_non_encapsulated (NCBI accession - HE651274)
• Add Group2_pspK_non_encapsulated (NCBI accession - JF48996)
• Add Group3_aliD_non_encapsulated (NCBI accession - JF490008)

Full Changelog: v2.0.1...v2.0.2

v2.0.1

What's Changed

• Minor changes including a fix for 19AF mistyping and updated documentation.

• add docker instructions by @Oliver-Lorenz-dev in #14
• fix for 19AF by @Oliver-Lorenz-dev in #15
• update documentation by @Oliver-Lorenz-dev in #16
• Update version by @Oliver-Lorenz-dev in #18

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

Update CTVdb

Added in new serotypes to the CTVdb (SeroBANK):
SeroBA can now detect 103 of 108 serotypes.

New serotypes:

11F_like
15D
20A
20B
20C
24C
33E
33H
36A
36B

New genetic variants:

6A-I
6A-II
6A-III
6A-IV
6A-V
6A-VI
6B-I
6B-II
19A-I
19A-II
19A-III
19F-I
19F-II
19F-III
19F-IV

Changed output file to CSV format

Sample,Serotype,Genetic_Variant,Contamination_Status

Full Changelog: v1.0.7...v2.0.0

v1.0.7

What's Changed

Renaming serotypes to updated names:

• Rename serogroup 20 to 20A - https://www.sciencedirect.com/science/article/pii/S0021925820478111

• Rename 39X to 10D - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240158/

• Rename 10X to 33G - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10782959/

Full Changelog: v1.0.6...v1.0.7

v1.0.6

What's Changed

• Bugfix release - Add in missing serotypes to database including 10X and 39X

Full Changelog: v1.0.5...v1.0.6

v1.0.5

What's Changed

• Updated KMC to version 3.2.2 (was 3.0.0 before) to fix some instability in the KMC software
• Cleanup Dockerfile and installation script

Full Changelog: v1.0.4...v1.0.5

v1.0.4

What's Changed

• Update seroBA database to use the latest PneumoCaT CTVdb (v1.2.1)
• Automated Docker Image Publish to Docker Hub and GitHub Packages at Releases

Full Changelog: v1.0.3...v1.0.4

v1.0.3

Creating this new fork for fixing SeroBA bugs and publish as Docker image, as the original repo is no longer maintained

What's Changed

• Add automated test on the resulting Docker Image on PR
• Fixing iteration over None error

Full Changelog: v1.0.2...v1.0.3