معرفی شرکت ها
covid-spike-classification-0.6.4
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مشاهده بیشترتوضیحات
Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | covid-spike-classification-0.6.4 |
| نام | covid-spike-classification |
| نسخه کتابخانه | 0.6.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Kai Blin |
| ایمیل نویسنده | kblin@biosustain.dtu.dk |
| آدرس صفحه اصلی | https://github.com/kblin/covid-spike-classification/ |
| آدرس اینترنتی | https://pypi.org/project/covid-spike-classification/ |
| مجوز | Apache Software License |
# Detect interesting SARS-CoV-2 spike protein mutations from Sanger sequencing data
[](http://bioconda.github.io/recipes/covid-spike-classification/README.html)
[](https://hub.docker.com/r/kblin/covid-spike-classification)
`covid-spike-classification` is a script to call interesting SARS-CoV-2 spike protein mutations
from Sanger sequencing to support the Danish COVID-19 monitoring efforts.
Using Sanger-sequenced RT-PCR product of the spike protein, this tool should pick up all relevant
mutations currently tracked (see [`covid_spike_classification/core.py`](https://github.com/kblin/covid-spike-classification/blob/main/covid_spike_classification/core.py#L15-L35)
for the full list of tracked mutations) and give a table with one row per sample and a
yes/no/failed column per tracked mutation.
This workflow is built and maintained at https://github.com/kblin/covid-spike-classification
If you found this tool useful, please cite https://www.medrxiv.org/content/10.1101/2021.03.27.21252266v1
## Installation
`covid-spike-classification` is distributed via this git repository, pypi or bioconda.
### Bioconda
Installing via bioconda is the fastest way to get up and running:
```sh
conda create -n csc -c conda-forge -c bioconda covid-spike-classification
conda activate csc
```
### git & pypi
When installing via git or pypi, you first need to install the external binary dependencies.
`covid-spike-classification` depends on three excellent tools to do most of the work:
* tracy (versions 0.5.3 & 0.5.7 tested)
* bowtie2 (version 2.4.2 tested)
* samtools (versions 1.10 & 1.11 tested)
If you have `conda` installed, the easiest way to get started is to just install these via calling
```sh
git clone https://github.com/kblin/covid-spike-classification.git
cd covid-spike-classification
conda env create -n csc -f environment.yml
conda activate csc
pip install .
```
### Docker, Podman, Singularity
While not technically an installation method, `covid-spike-classification` is also shipped as an OCI container.
To use it, you ideally run the container from a workflow management system like [Snakemake](https://snakemake.github.io/)
or [Nextflow](https://www.nextflow.io/) that will take care of mounting filesystems into the container for you.
The OCI container image is available from the Docker Hub [`kblin/covid-spike-classification`](https://hub.docker.com/r/kblin/covid-spike-classification)
repository.
## Setup
You also need to generate the samtools and bowtie2 indices for your reference genome. We ship a
copy of NC\_045512 and a script to generate these indices:
```sh
conda activate csc
cd ref
./build_indices.sh
cd ..
```
## Usage
Assuming you used above instructions to install via conda, you can run the tool like this:
```sh
conda activate csc
covid-spike-classification --reference /path/to/your/reference.fasta --outdir /path/to/result/dir /path/to/sanger/reads/dir_or.zip
```
Notably, you can provide the input either as a ZIP file or as a directory, as long as they directly contain the ab1 files you want
to run the analysis on.
See also the `--help` output for more detailed usage information.
## License
All code is available under the Apache License version 2, see the
[`LICENSE`](LICENSE) file for details.
نیازمندی
| مقدار | نام |
|---|---|
| - | biopython |
| - | flake8 |
| - | pytest |
نحوه نصب
نصب پکیج whl covid-spike-classification-0.6.4:
pip install covid-spike-classification-0.6.4.whl
نصب پکیج tar.gz covid-spike-classification-0.6.4:
pip install covid-spike-classification-0.6.4.tar.gz