gauravearn / graphanalyzer

a graphanalyzer package that uses the information from the paf and the gfa files for the graph alignment and uses the concurrency to process the alignments and other variables and uses a dataframe approach

graphanalyzer

a graphanalyzer package that uses the information from the paf and the gfa files for the graph alignment and uses the concurrency to process the alignments and other variables and uses a dataframe approach. You can find the code in the src/graphanalyzer.py and you can use those as import in your script untill the complete package is available from pip. a heuristic binary search implementation of the node in the graph clustering. It follows the stack implementation so that that the weight to the next node can be assigned on the search pattern. Written in a combination of C++ and python. Added the support for the visualization of graphics. Update: 2024-3-1: Adding the support for the deadlock programming to enable the multi threads. Adding the complete support for analyzing all the PAF, GFA and also the LAV files from the alignment for the index similarity. Update: 2024-3-12: Adding the support for the graph linearization for direct import to view the pangenome graphs in the linear format.

Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany

Installation

$ pip install graphanalyzer

License

graphanalyzer was created by Gaurav Sablok, Universitat Potsdam, Germany. It is licensed under the terms of the MIT license.

Credits

graphanalyzer was created with cookiecutter and the py-pkgs-cookiecutter template.