https://github.com/anuradhawick/graphplas

GraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from TGS Assemblies
https://github.com/anuradhawick/graphplas

Last synced: 18 days ago
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GraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from TGS Assemblies

• Host: GitHub
• URL: https://github.com/anuradhawick/graphplas
• Owner: anuradhawick
• License: mit
• Created: 2020-08-14T08:08:51.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2022-07-12T08:13:30.000Z (almost 3 years ago)
• Last Synced: 2025-05-07T08:03:11.713Z (18 days ago)
• Language: Python
• Size: 1.45 MB
• Stars: 6
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# GraphPlas

GraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from NGS Assemblies

![GraphPlas logo](GraphPlas.png)

# Usage Instructions

```

usage: GraphPlas [-h] --spades-path SPADES_PATH --classifier CLASSIFIER

                 --classification-file CLASSIFICATION_FILE --output OUTPUT

                 [--threads THREADS] [--min_contig_length MIN_CONTIG_LENGTH]

                 [--plots] [--version] [--ground-truth GROUND_TRUTH]

GraphPlas Plasmid Detection Using Assembly Graph

optional arguments:

  -h, --help            show this help message and exit

  --spades-path SPADES_PATH, -s SPADES_PATH

                        Assembly path

  --classifier CLASSIFIER, -c CLASSIFIER

                        Classifier [pc or pf] default=pc

  --classification-file CLASSIFICATION_FILE, -f CLASSIFICATION_FILE

                        Path to classification file

  --output OUTPUT, -o OUTPUT

                        Output directory

  --threads THREADS, -t THREADS

                        Thread limit

  --min_contig_length MIN_CONTIG_LENGTH, -m MIN_CONTIG_LENGTH

                        Minimum length of contigs to consider

  --plots               Whether to plot the graph images

  --version, -v         Show version.

  --ground-truth GROUND_TRUTH, -i GROUND_TRUTH

                        Ground truths file (tab separated file with contig_id

                        and truth label on each line). Plasmid label =

                        plasmid, Chromosome label = chromosome

```

## Notes

* The program can get significantly slow if the assembly has many small contigs, disconnected from classified contigs. The minimum contig length can be adjusted using `--min_contig_length` parameter. We now set it at 500 by default. 

## Citation

If you use this tool/approach in your work consider using the below citation.

```

@ARTICLE{9439922,

  author={Wickramarachchi, Anuradha and Lin, Yu},

  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, 

  title={GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs}, 

  year={2021},

  volume={},

  number={},

  pages={1-1},

  doi={10.1109/TCBB.2021.3082915}}

```