Referenceseeker Versions Save

This is the 8th minor release (v1.8.0) introducing adjustable sliding windows.

New features:

• Implement adjustable sliding windows for the DNA fragment creation: #24

Improvements:

• fix RefSeq db build scripts: https://github.com/oschwengers/referenceseeker/commit/d662dc5f27194c7f2645f815b348408c5a677f16

This is a patch release:

• fixing several minor issues (#19) regarding the creation of custom DBs
• adding more CI tests

This is a feature release providing:

• massively reduced database sizes due to compressed reference genomes
• allow for zipped input genomes
• new pre-compiled databases from GTDB and PLSDB

As well as:

• new tests
• move to Python 3.8 as default

As we currently have no infrastructure to test & debug the tool on MacOS, we skipped the integration tests on MacOS. Any suggestions/support is highly welcome.

This is a patch release fixing several DB creation issues.

• fixed an index issue upon unnamed DB records (#13)
• fixed 3rd party binary paths upon DB imports
• update CI/CD scripts

This is just a minor patch to remove some debugging artifacts.

This is a minor release fixing broken 3rd party dependencies in the share directory. This issue is masked within a BioConda environment.

This is the first minor release after the JOSS publication.

We updated the pre-compiled RefSeq databases and fixed some minor typos and bugs.

This release archives the to-be-published version 1.6 necessary for the JOSS publication.

In this release we:

• added a CONTRIBUTING.md
• added issue templates for bugs and features
• fixed some typos

This release provides an exciting new feature: ReferenceSeeker now supports the initialization of local, private & custom DBs and the fine grained import of local genomes - either into a fresh new DB or an existing public one. Therefore, check the new referenceseeker_db command - more info in the readme DB section

Additionally, we:

• added a tiny mock DB as a test case -> assure your local installation works as expected!
• improved the documentation (readme)
• applied some code refactoring
• added PyTest-based unit tests
• implemented a GitHub Actions-based CI -> further code quality assurance

This release introduces the bidirectional computation of ANI / conserved DNA values.

Just add the --bidirectional option.