v1.2.0

1.2.0 (2025-01-20)

Features

• allow masking with custom ref (d436eae)

Bug Fixes

• updated dependency issues in main environment (7971c7a)

v1.1.2

1.1.2 (2024-04-26)

Bug Fixes

• Fix type error doing dryrun with fixed reference (8539c88)

v1.1.1

1.1.1 (2024-02-23)

Bug Fixes

• add hpc resources (b15eaed)
• convert hpc config values to int (55e5656)
• improve error message for outlier genomes (2c038b4)

v1.1.0

1.1.0 (2024-02-23)

Features

• add QC per cluster (65960ef)
• allow toggling snippy --report flag (0949a61)

Bug Fixes

• allow gbk and fasta refs (7dbea61)

v1.0.0

1.0.0 (2024-02-21)

⚠ BREAKING CHANGES

• update juno library to v2

Code Refactoring

• update juno library to v2 (347971f)

v0.0.3

0.0.3 (2023-12-05)

Bug Fixes

• rm unneeded rules (5df54ff)
• set prefix to str (89ea436)

Dependencies

• re-add containers (3930b55)

Documentation

• update README (6dcb6c6)

v0.0.2

0.0.2 (2023-07-24)

Bug Fixes

• fix environments (7e2857e)

Dependencies

• clean up envs (4eab33e)
• fix dependencies for multiple environments/tools (3f8e2e6)
• remove anaconda and defaults channel and add nodefaults (84d6132)

First release

Juno-SNP is a toolkit for performing SNP comparison based on a set of reads and assemblies (e.g. Juno-assembly output).

Features include:

• Snippy mapping, generation of a SNP matrix and inference of UPGMA and ML trees
• Preclustering using mash: this ensures divergent samples are not mapped to a single references, but are split into several clusters
• Provide your own reference genome or let referenceseeker choose one for you.
• Dependencies are managed using conda. Singularity support will be restored later.
• Generation of an audit trail