ReferenceSeeker - v1.8.0

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 4 years ago

ReferenceSeeker - v1.7.3

This is a patch release: - fixing several minor issues (#19) regarding the creation of custom DBs - adding more CI tests

Scientific Software - Peer-reviewed - Python
Published by oschwengers about 5 years ago

ReferenceSeeker - v1.7.1

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.

Scientific Software - Peer-reviewed - Python
Published by oschwengers about 5 years ago

ReferenceSeeker - v1.6.4

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 5 years ago

ReferenceSeeker - v1.6.3

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers about 6 years ago

ReferenceSeeker - v1.6.2

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers about 6 years ago

ReferenceSeeker - v1.6.1

This is the first minor release after the JOSS publication.

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers about 6 years ago

ReferenceSeeker - v1.6

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 6 years ago

ReferenceSeeker - v1.5

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

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 6 years ago

ReferenceSeeker - v1.4

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

Just add the --bidirectional option.

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 6 years ago

ReferenceSeeker - v1.3

Added options: - --ani: set custom ANI threshold (default=0.95) - --conserved-dna: set custom conserved DNA threshold (default=0.69)

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 6 years ago

ReferenceSeeker - v1.2.0

This is release is a purely technical update: - ReferenceSeeker is now on PyPI (https://pypi.org/project/referenceseeker/) - we dropped any Docker image support - we dropped the scaffolding feature via MeDuSa in order to speedup a subsequent BioConda migration.

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 6 years ago

ReferenceSeeker - v1.1.0

Changes

• Added option to select numbers of candidate reference genomes to assess
• Output N50/L50 statistics after scaffolding contigs
• Added Mash distance values to output

Bug fixes

• Fixed MeDuSa Python3 dependencies
• Added Java dependency to Dockerfile

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 7 years ago

ReferenceSeeker - v1.0.1

This is a minor patch release fixing a MeDuSa related bug due to a missing MUMmer/show-coords binary.

Scientific Software - Peer-reviewed - Python
Published by oschwengers over 7 years ago