phables 1.3.3

What's Changed

• Adding dockerfile by @linsalrob in #51
• Updated database paths for download
• Minor bug fixes

New Contributors

• @linsalrob made their first contribution in #51

Full Changelog: v1.3.2...v1.3.3

phables 1.3.2

What's Changed

• Updated environment files

Full Changelog: v1.3.1...v1.3.2

Please report any issues and suggestions under Phables Issues.

phables 1.3.1

What's Changed

• You can now add a prefix for your genomes names.
• Updated genome path format in the resolved_genome_info.txt. Now the unitigs of the genome are represented as unitig_name:orientation,unitig_name:orientation,... where orientation can be fwd/rev.
• Minor bug fixes

Full Changelog: v1.3.0...v1.3.1

Please report any issues and suggestions under Phables Issues.

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: v1.2.2...v1.3.0

Please report any issues and suggestions under Phables Issues.

phables 1.2.2

What's Changed

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

Full Changelog: v1.2.1...v1.2.2

Please report any issues and suggestions under Phables Issues.

phables 1.2.1

What's Changed

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

Full Changelog: v1.2.0...v1.2.1

Please report any issues and suggestions under Phables Issues.

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: v1.1.0...v1.2.0

Please report any issues and suggestions under Phables Issues.

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: v1.0.0...v1.1.0

Please report any issues and suggestions under Phables Issues.

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: v0.2.0...v1.0.0

Please report any issues and suggestions under Phables Issues.

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.