https://github.com/wglab/infuse
Software for detecting gene fusions and exon-skippings from long read sequencing
https://github.com/wglab/infuse
Last synced: 6 months ago
JSON representation
Software for detecting gene fusions and exon-skippings from long read sequencing
- Host: GitHub
- URL: https://github.com/wglab/infuse
- Owner: WGLab
- Created: 2024-07-02T19:50:40.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-03-11T21:34:37.000Z (over 1 year ago)
- Last Synced: 2025-03-11T22:25:23.810Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 43.9 KB
- Stars: 0
- Watchers: 6
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# InFuse
InFuse: gene fusion and exon-skipping detection from long read sequencing (under construction)
## Installation
```
git clone https://github.com/WGLab/InFuse.git
pip install numpy pandas numba sklearn pysam ncls numpy_indexed parasail
python InFuse/InFuse.py --help
```
## Usage
For gene fusion detection, please run the following command:
`python PATH_TO_INFUSE_REPO/InFuse.py --bam BAM_FILE --output OUTPUT_FOLDER --prefix PREFIX --gff GFF_ANNOTATION_FILE --transcripts TRANSCRIPT_FASTA_FILE --threads NUM_THREADS --min_support MIN_READS --distance_threshold DISTANCE_THRESHOLD --gf_only`
where BAM_FILE is an aligned BAM file, GFF_ANNOTATION_FILE is genome annotation GFF3 file, TRANSCRIPT_FASTA_FILE is a FASTA file containing spliced transcript sequences from the GFF3 file, NUM_THREADS is the number of threads to use for multiprocessing speedup, MIN_READS specifies the minimum read support needed for reporting a gene fusion, and DISTANCE_THRESHOLD specifies the distance in bp for merging gene fusion breakpoints.
The output folder will contain a tab seperated file `PREFIX.final_gf_double_bp` containing all gene fusions, as well as a python pickle file `PREFIX.final_gf_double_bp.pickle` containing detailed read-level information for all gene fusions.