NeatSeq-Flow’s Module and Workflow Repository¶
NeatSeq-Flow is a lightweight software for efficient execution of high throughput sequencing workflows. See the NeatSeq-Flow documentation at http://neatseq-flow.readthedocs.io/en/latest/.
NeatSeq-Flow is available for download on github.
Following is a list of modules included in this repository.
In order to include these modules in your workflow, please:
download the repository:
Alternatively, clone the repository:
git clone https://github.com/bioinfo-core-BGU/neatseq-flow-modules.git
add the following line in the Global_params section of your workflow parameter file:
See more about definition of workflow parameter files in the documentation for the main NeatSeq-Flow package at http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#parameter-file-definition.
Some of the modules in this package are included in the main NeatSeq-Flow repository. These are indicated below with a *.
NeatSeq-Flow enables users to program their own modules and workflows. You are encouraged to share your modules with the public by adding it to this repository. In order to do so, please fork the repository on github, upload your new module or workflow and open a pull request.
- Preparation and QC
- BAM Conversion to Other Formats
- Genome Assembly
- Transcriptome Assembly
- Transcriptome Annotation
- Sequence Annotation
- Sequence-Searching Related Tasks
- Variant-related Tasks
- QIIME (version 1.9)
- Sequence Clustering
- Various Reporting Programs
- Miscellaneous Modules
- Generic Module