GraphBin v1.7.1

• Change python-igraph to igraph on PyPI release.
• Update conda env to use cogent3 from PyPI so numba version is resolved properly depending on the python version.
• Includes minor refactoring and bug fixes.

Full Changelog: v1.7.0...v1.7.1

Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.7.0

• Refactor code to re-use common logic
• Replace argparse with click.
• Includes minor refactoring and bug fixes.

Full Changelog: v1.6.1...v1.7.0

Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.6.1

• Updated the process of building graphs for MEGAHIT and Flye graphs.
• Includes minor refactoring and bug fixes.

Full Changelog: v1.6.0...v1.6.1

Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.5

• Updated the process of removing labels of ambiguous vertices to stop removing entire bins
• Includes minor refactoring and bug fixes.

Full Changelog: v1.4...v1.5

Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.4

• Fixed issue with reading bin ids.
• Fixed naming of SPAdes contigs to have original contig identifiers and updated prepResult.py to reflect this fix.
• Added functionality to provide a delimiter for input/output results
• Includes minor refactoring and bug fixes.

Full Changelog: v1.3...v1.4

Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.3

• Added validation to check whether the initial binning result contains contigs belonging to multiple bins.
• Updated log levels and log messages.
• Includes minor refactoring and bug fixes.
• Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.2

• Updated Conda installation. Please refer to the README file for updated commands.
• Added pip installer. Please refer to the README file for installation steps and running commands.
• Fixed errors with MEGAHIT version to support original k<>_* contig naming.
• Added support to process binning results with .fna files.
• Includes minor refactoring and bug fixes.
• Please report any issues and suggestions under GraphBin Issues.

GraphBin v1.1

• Added support for Flye, Canu and Miniasm long-read assemblies.
• Includes minor bug fixes.
• Please report any issues and suggestions under GraphBin Issues.

Note: We have developed GraphBin for Illumina short reads and the long-read assemblies might have sparsely connected graphs. This can make the label propagation less effective and may not result in improvements.

GraphBin v1.0

• This is the first stable release of GraphBin.
• Added Conda environment for GraphBin.
• Please report any issues and suggestions under GraphBin Issues.

GraphBin v0.2

• This is the second pre-release of GraphBin.
• Included support for MEGAHIT assemblies.
• Added the functionality to run SPAdes, SGA and MEGAHIT scripts from one single script.
• This release may contain bugs and unhandled errors.
• Please report any issues and suggestions under GraphBin Issues.