phables - phables 1.4.1

What's Changed

• Supports only MacOS and Linux from now on as some dependencies are not available for Windows.

Full Changelog: https://github.com/Vini2/phables/compare/v1.4.0...v1.4.1

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 1 year ago

phables - phables 1.4.0

• Now supports the resolution of linear components with multiple sources and sinks.
• Minor bug fixes and code formatting

Full Changelog: https://github.com/Vini2/phables/compare/v1.3.3...v1.4.0

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 almost 2 years ago

phables - phables 1.3.3

What's Changed

• Adding dockerfile by @linsalrob in https://github.com/Vini2/phables/pull/51
• Updated database paths for download
• Minor bug fixes

New Contributors

• @linsalrob made their first contribution in https://github.com/Vini2/phables/pull/51

Full Changelog: https://github.com/Vini2/phables/compare/v1.3.2...v1.3.3

- Python
Published by Vini2 almost 2 years ago

phables - phables 1.3.2

What's Changed

• Updated environment files

Full Changelog: https://github.com/Vini2/phables/compare/v1.3.1...v1.3.2

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 about 2 years ago

phables - phables 1.3.1

What's Changed

• You can now add a prefix for your genomes names.
• Minor bug fixes

Full Changelog: https://github.com/Vini2/phables/compare/v1.3.0...v1.3.1

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 about 2 years ago

phables - phables 1.3.0

What's Changed

• Phables can now resolve phage genomes from long-read assemblies.
• You can run Phables on long-read assemblies of phage isolate as well.

Full Changelog: https://github.com/Vini2/phables/compare/v1.2.2...v1.3.0

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 2 years ago

phables - phables 1.2.2

What's Changed

• Resolves linear phage genomes with DTRs.
• Output files are now organised for each processing step.

Full Changelog: https://github.com/Vini2/phables/compare/v1.2.1...v1.2.2

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 2 years ago

phables - phables 1.2.1

What's Changed

• Minor updates to postprocessing rules.
• Minor bug fixes and code refactoring.

Full Changelog: https://github.com/Vini2/phables/compare/v1.2.0...v1.2.1

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 2 years ago

phables - phables 1.2.0

What's Changed

• Now phables can recover linear phage genomes from complex linear components.
• Added postprocessing steps for resolved genomes.
• Multi-threading for Gurobi MFD solver.
• Minor bug fixes and code refactoring.

Full Changelog: https://github.com/Vini2/phables/compare/v1.1.0...v1.2.0

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 almost 3 years ago

phables - phables 1.1.0

• Revert to use coverm to calculate mean unitig coverage.
• Update flow decomposition modelling.
• Add functionality to recover singleton linear contigs
• Minor bug fixes and code refactoring.

Full Changelog: https://github.com/Vini2/phables/compare/v1.0.0...v1.1.0

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 almost 3 years ago

phables - phables 1.0.0

• This is the first stable release of Phables.
• Replace coverm with minimap2 and awk to calculate contig coverage.
• Add more information about the components from which genomes are resolved.
• Fix code to identify terminal repeats.
• Minor bug fixes and code refactoring.

Full Changelog: https://github.com/Vini2/phables/compare/v0.2.0...v1.0.0

Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 about 3 years ago

phables - phables 0.2.0

• Updated scan for PHROGs in components.
• Minor bug fixes and code refactoring.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.1

• Combine preprocessing and run steps to one command.
• This release may still contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.0

• Support for any assembly graph in GFA format
• Handling of temporary files for CoverM
• This release may still contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.0b7

• This is the first beta release of Phables.
• Used Snaketool to combine the preprocessing steps and main code into an easy-to-use pipeline.
• This release may still contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.0a3

• This alpha release includes bug fixes of Phables.
• This release may still contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.0a2

• This is the second alpha release of Phables.
• networkx version pinned to 2.8.6 or above as bfs_layers was introduced from version 2.8.6.
• This release may contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago

phables - phables 0.1.0a1

• This is the first alpha release of Phables.
• This release may contain bugs and unhandled errors.
• Please report any issues and suggestions under Phables Issues.

- Python
Published by Vini2 over 3 years ago