viroprofiler

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

(★ 39)

A containerized bioinformatics pipeline for viral metagenomic data analysis

viroprofiler 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
[![DOI](https://zenodo.org/badge/537899739.svg)](https://zenodo.org/badge/latestdoi/537899739)

```
                                        __
oooooo     oooo oo                    88  88                    .o8o.  oo  ooo
 `888.     .8'  `'                   88 ss 88                   88 `"  `'  `88
  `888.   .8'  ooo  ooood8b  o888o    88__88   ooooo8b  o888o  o88o   ooo   88   .oooo.  ooooo8b
   `888. .8'   `88   88""8P d8' `8b     ||      88""8P d8' `8b  88    `88   88  d8'  `8b  88""8P
    `888.8'     88   88     88   88    _||_     88     88   88  88     88   88  888ooo88  88
     `888'      88   88     88   88  // || \\   88     88   88  88     88   88  88    .o  88
      `8'      o88o o88b     o888o  //      \\ d88b     o888o  o88o   o88o o88o `Y8bd8P' 088b

```

## Introduction

ViroProfiler is a bioinformatics best-practice analysis pipeline for viral metagenomics data analyses.

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.

![viroprofiler workflow](https://raw.githubusercontent.com/deng-lab/viroprofiler/main/docs/images/viroprofiler.png)

## Quick Start

1. Install one of the supported container engines using **root** privileges:

- [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps)
   - [Charliecloud](https://hpc.github.io/charliecloud/install.html)
   - [Docker](https://docs.docker.com/install/)
   - [Podman](https://podman.io/getting-started/installation)
   - [Shifter](https://github.com/NERSC/shifter)

2. Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html).

3. Install Nextflow using conda:

```bash
   # You may need to restart your terminal before running the following commands
   conda install -c bioconda nextflow
   ```

4. Download the pipeline and database.

```bash
   # setup database
   nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup"
   ```

`-profile` specifies the container engine to use. You can use `singularity`, `charliecloud`, `docker`, `podman`, or `shifter`. You can also use `test` to run the pipeline with test data after setting up the database.

5. Run the pipeline,

```bash
   # run test
   nextflow run deng-lab/viroprofiler -r main -profile singularity,test

# run your own data
   nextflow run deng-lab/viroprofiler -r main -profile singularity --input samplesheet.csv
   ```

6. Update the pipeline,

```bash
   nextflow pull deng-lab/viroprofiler
   ```

Please refer to the [tutorial](https://deng-lab.github.io/viroprofiler/tutorial) for more information on how to run the pipeline with customized parameters and options.

## Documentation

Please refer to the [documentation](https://deng-lab.github.io/viroprofiler).

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

For further information or help, please [open an issue](https://github.com/deng-lab/viroprofiler/issues).

## Citations

If you use  ViroProfiler for your analysis, please cite the publication as follows:

> *Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng*. **ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis**. *Gut Microbes* (2023); doi: https://doi.org/10.1080/19490976.2023.2192522

An extensive list of references for the tools and data used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. If you use ViroProfiler for your work, please cite the relevant references.

viroprofiler

viroprofiler 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

viroprofiler

viroprofiler 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README