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sashimi.py
what is sashimi.py
sashimi.py is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
Features of sashimi.py
- Support various file formats as input
- Support strand-aware coverage plot
- Visualize coverage by heatmap, including HiC diagram
- Visualize protein domain based the given gene id
- Demultiplex the single-cell RNA/ATAC-seq which used cell barcode into cell population
- Support visualizing individual full-length reads in read-by-read style
- Support visualize circRNA sequencing data
Input
sashimi.py supports almost NGS data format, including
- BAM
- Bed
- bigBed
- bigWig
- Depth file generated by
samtools depth
- naive Hi-C format
Output
The output will be a pdf and other image file formats which satisfy the requirement of the major journals, and each track on output corresponds these datasets from config file.
Usage
The sashimi.py is written in Python, and user could install it in a variety of ways as follows
Note: if segment fault
with multiple processing, please try to use docker image, or just run with -p 1
.
-
install from PiPy
pip install sashimi.py
-
install from bioconda
conda install -c bioconda sashimi-py # or conda env create -n sashimi -f environment.yaml # or conda env create -n sashimi -c conda-forge -c bioconda -f requirements.txt conda activate sashimi && python setup.py install
-
using docker image
docker pull ygidtu/sashimi docker run --rm ygidtu/sashimi --help # or git clone from https://github.com/ygidtu/sashimi.py sashimi cd sashimi docker build -t ygidtu/docker . docker run --rm ygidtu/sashimi --help
-
install from source code
git clone https://github.com/ygidtu/sashimi.py sashimi cd sashimi python setup.py install sashimipy --help # pr python main.py --help
-
running from a local webserver
git clone https://github.com/ygidtu/sashimi.py sashimi cd sashimi/web # build the frontend static files npm install -g vue-cli vite && npm install vite build # prepare the backend server pip install fastapi pydantic jinja2 uvicorn python server.py --help
-
for
pipenv
usersgit clone https://github.com/ygidtu/sashimi.py cd sashimi.py pipenv install # create virtualenv and install required packages pipenv shell # switch to virtualenv sashimipy --help # pr python main.py --help
Example
python main.py \
-e chr1:1270656-1284730:+ \
-r example/example.sorted.gtf.gz \
--interval example/interval_list.tsv \
--density example/density_list.tsv \
--show-side \
--igv example/igv.tsv \
--heatmap example/heatmap_list.tsv \
--focus 1272656-1272656:1275656-1277656 \
--stroke 1275656-1277656:1277856-1278656@blue \
--sites 1271656,1271656,1272656 \
--line example/line_list.tsv \
-o example/example.png \
--dpi 300 \
--width 10 \
--height 1 \
--barcode example/barcode_list.tsv \
--domain --remove-duplicate-umi
here is the output file.
Questions
Visit issues or contact Yiming Zhang and Ran Zhou
Citation
If you use Sashimi.py in your publication, please cite Sashimi.py by
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