NeatSeq-Flow’s Module and Workflow Repository

This repository contains modules and workflows for use with NeatSeq-Flow. To install, follow the instructions in installation section bellow.

See also the main NeatSeq-Flow website.

Workflows

• NeatSeq-Flow Tutorial Workflow
• RNA-Seq analysis for non-model organisms
• RNA-Seq using a reference genome
• Transcriptome assembly and annotation with Trinity
• Microbiome analysis using QIIME
• Microbiome analysis using QIIME2
• Variant analysis using GATK
• Microbe-Flow: a comprehensive workflow for bacterial genomics, pathogenomics and genomic epidemiology
• ChIP-seq workflow
• Shotgun Metagenomics

Modules

• NeatSeq-Flow modules
  • Preparation and QC
  • Mapping
  • BAM Conversion to Other Formats
  • ChIP-seq
  • Genome Assembly
  • Transcriptome Assembly
  • Transcriptome Annotation
  • RNASeq
  • Sequence Annotation
  • Sequence-Searching Related Tasks
  • Variant-related Tasks
  • Metagenomics
  • Microbiology
  • QIIME (version 1.9)
  • QIIME (version 2)
  • GATK
  • Sequence Clustering
  • Various Reporting Programs
  • Miscellaneous Modules
  • Generic Modules

Tutorials

• Using The Generic Module

Installing and using the modules

NeatSeq-Flow is available for download on github.

Attention

In order to include these modules in your workflow, please:

1. download the repository:

   curl -LO https://github.com/bioinfo-core-BGU/neatseq-flow-modules/archive/master.zip
   

2. Alternatively, clone the repository:

   git clone https://github.com/bioinfo-core-BGU/neatseq-flow-modules.git
   

3. add the following line in the Global_params section of your workflow parameter file:

   module_path: /path/to/location/of/modules/repository
   

See more about definition of workflow parameter files in the NeatSeq-Flow User Manual at the Parameter file definition section.

Note

Some of the modules in this package are included in the main NeatSeq-Flow repository. These are indicated below with a ^*.

Important

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.