Dear Community,
After careful consideration, we have decided to shift our focus to new and innovative initiatives that will better serve our community and align with our long-term goals.
Effective Date: May 12th, 2025
Impact on Users:
- The project repository will be archived and set to read-only mode, ensuring that it remains accessible for reference.
- While no further updates, bug fixes, or support will be provided, we encourage you to explore the wealth of knowledge and resources available in the repository.
- Existing issues and pull requests will be closed, but we invite you to engage with other projects and contribute your expertise.
Licensing: The project will remain under its current open-source license, allowing others to fork and continue development if they choose.
We understand that this change may come as a surprise, but we are incredibly grateful for your support and contributions over the years. Your dedication has been instrumental in the success of this project, and we look forward to your continued involvement in our future endeavors.
Thank you for your understanding and support.
nf-HAVoC is a bioinformatic pipeline designed to provide an accessible tool for constructing consensus sequences from SARS-CoV-2 FASTQ files and identifying the variants they belong to. The pipeline is an implementation of HAVoC (DOI: https://doi.org/10.1186/s12859-021-04294-2) and built on Nextflow, 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.
nf-HAVoC can be run to analyze FASTQ files within a directory/
The target directory must contain matching FASTQ files for forward (R1) and reverse (R2) reads, which can be either gzipped (*.fastq.gz) or uncompressed (*.fastq).
The following options can be changed as commandline options depending on your preferences:
| Option | Input | Function |
|---|---|---|
| prepro | fastp* or trimmomatic | Tool for pre-processing FASTQ files. |
| aligner | bowtie or bwa* | Tool for aligning reads. |
| sam | sambamba* or samtools | Tool for SAM/BAM processing |
| coverage | Number (30*) | Minimum coverage for masking regions in consensus sequence. |
| pangolin | yes* or no | Run Pangolin for lineage identification. |
* By default.
Only one tool can be utilized per option.
-
Install
Nextflow(>=20.10.0) -
Install any of
Docker -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run microsoft/nf-HAVoC -profile local --nextera 'path/to/NexteraPE-PE.fa' --ref path/to/ref.fa' --reads 'path/to/fastq/*R{1,2}*fastq.gz' = -
Start running your own analysis on Azure.
Azure Batch Setup
Please refer to the Nextflow documentation which describe how to setup the Azure Batch environment.
```console
nextflow run microsoft/nf-HAVoC -profile azure --nextera 'az://coantiner/NexteraPE-PE.fa' --ref 'az://container/ref.fa' --reads 'az://container/*R{1,2}*fastq.gz' -w 'az://conatiner/work'
```
* Azure speicifcs can be changed in the config locally or provided as commandline options*
These scripts were originally found Original Code. For more information visit Webpage Helsinki university Analyzer for Variants of Concern.
This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.
This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.
Copyright (C) 2022 Microsoft Corporation.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow