diff --git a/README.md b/README.md index 681604d..b260b7d 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,9 @@ # PANCAT - PANgenome Comparison and Anlaysis Toolkit +> [!WARNING]\ +> A paper is in preparation about this work. If you consider to use this tool, please contact the author for attribution. + Implementations of many functions for performing various actions on GFA-like graphs in a command-line tool, such as extracting or offseting a pangenome graph. Is capable of comparing graphs topology between graphs that happen to contain the same set of sequences. Does pangenome graphs visualisation with interactive html files. Uses the [gfagraphs library](https://pypi.org/project/gfagraphs/) to load and manipulate pangenome graphs. @@ -42,11 +45,15 @@ Other tools are in the `scripts` folder. Are available through `pancat`: - **offset** adds relative position information as a tag in GFA file +- **correct** (WIP, experimental) corrects the graph by adding missing information back into it. - **grapher** creates interactive graph representation from a GFA file +- **multigrapher** creates interactive graph representation of the differnces between two pangenome graphs - **stats** gathers basic stats from the input GFA - **complete** assesses if the graph is a complete pangenome graph (all genomes fully embedded in the graph) - **reconstruct** recreates the linear sequences from the graph - **edit** computes a edit distance between variation graphs +- **compress** (WIP, experimental) compresses the graph by collapsing substitution bubbles, losselessly +- **unfold** (WIP, experimental) break cycles in the graph by adding nodes and edges in it Were available before (and will be back soon): - **isolate** extracts a subgraph from positions in the paths diff --git a/setup.py b/setup.py index 9ebf511..9173e5a 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ setup( name=NAME, - version='0.2.0', + version='0.3.0', description='Tools for manipulating and visualizing GFA file format', url='https://github.com/Tharos-ux/pancat', author='Tharos',