https://github.com/sciencegenome/pangenome-graph-combiner

rust pangenome graph asm
https://github.com/sciencegenome/pangenome-graph-combiner

bioinformatics bioinformatics-pangenome-graphs genome-analysis-annotation graphs-algorithms pangenome pangenome-graph

Last synced: 3 months ago
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rust pangenome graph asm

• Host: GitHub
• URL: https://github.com/sciencegenome/pangenome-graph-combiner
• Owner: sciencegenome
• License: mit
• Created: 2025-01-14T19:28:33.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2025-01-17T22:31:29.000Z (5 months ago)
• Last Synced: 2025-01-24T19:37:17.467Z (5 months ago)
• Topics: bioinformatics, bioinformatics-pangenome-graphs, genome-analysis-annotation, graphs-algorithms, pangenome, pangenome-graph
• Language: Rust
• Homepage:
• Size: 3.14 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# rust-pangenome-graph-combiner

 - rust pangenome linerarization and combination approach

 - writes the 0 segment approach as asm for the minigraph alignment.

 - please see the last commit message and if it says compiled binary then it is completed or else still in development version.

 ```

 cargo build

 

 ```

 ```

 ╭─gauravsablok@fedora ~/Desktop/work/rust-pangenome-graph-combiner  ‹main*› 

 ╰─➤  ./target/debug/rust-pangenome-graph-combiner -h

 Usage: rust-pangenome-graph-combiner 

  Arguments:

    please provide the path to the graph file

 Options:

  -h, --help     Print help

  -V, --version  Print version

 

 ```

 - to run the binary 

 ```

 ╭─gauravsablok@fedora ~/Desktop/rust/pangenome-graph-combiner  ‹main*›

 ╰─➤  ./rust-pangenome-graph-combiner ./sample-file/sample-pangenome.gfa

 L       MTh0    0       +       MTh4001 4001    +       0M      SR:i:0  L1:i:4001       L2:i:501

 L       MTh4001 4001    +       MTh4502 4502    +       0M      SR:i:0  L1:i:501        L2:i:5003

 L       MTh4502 4502    +       MTh9505 9505    +       0M      SR:i:0  L1:i:5003       L2:i:3509

 L       MTh9505 9505    +       MTh13014        13014   +       0M      SR:i:0  L1:i:3509       L2:i:502

 L       MTh13014        13014   +       MTh13516        13516   +       0M      SR:i:0  L1:i:502        L2:i:3053

 Results have been written:graph asm have been written

 Gaurav Sablok