anadama_workflows

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AnADAMA Workflows

AnADAMA Workflows is a set of the most commonly used microbial community analysis pipelines run with AnADAMA (Another Automated Data Analysis Management Application). AnADAMA Workflows allows you to easily and quickly process 16S rDNA amplicon and WGS sequence data. There are 5 pipelines available in AnADAMA Workflows: SixteenS, USearch16S, WGS, RNA, and Visualization.

Getting Started with AnADAMA Workflows

General Requirements

  1. Python (version >= 2.7)
  2. AnADAMA (automatically installed)
  3. Operating system (Linux or Mac)

Requirements for the SixteenS and USearch16S pipelines

  1. QIIME
  2. PICRUSt
  3. EAUtils
  4. USEARCH (Required for the USearch16S pipeline only)

Requirements for the WGS pipeline

  1. KneadData
  2. MetaPhlAn2
  3. HUMAnN2

Requirements for the RNA pipeline

  1. SUBREAD
  2. SAMTools

Requirements for the Visualization pipeline

  1. QIIME
  2. MaAsLin
  3. BreadCrumbs

For detailed instructions on how to install the dependencies for each pipeline, please see the AnADAMA Workflows User Manual installation section.

Installation

Download and install AnADAMA Workflows:

  1. Download the software
  2. Unpack the software and change directories
    • $ tar zxvf anadama_workflows.tar.gz
    • $ cd anadama_workflows
  3. Edit the settings file to add the locations of your databases
  4. Install the software
    • $ python setup.py install
    • If you do not have write permissions to '/usr/lib/', then add the option "--user" to the install command. This will install the python package into subdirectories of '~/.local'. Please note when using the "--user" install option on some platforms, you might need to add '~/.local/bin/' to your $PATH as it might not be included by default. You will know if it needs to be added if you see the following message anadama: command not found when trying to run AnADAMA Workflows after installing with the "--user" option.

How to run

Basic usage

Pipelines are run with the following command:
$ anadama pipeline pipelineName
where pipelineName is the name of the pipeline.

To find out information about a specific pipeline, run:
$ anadama help pipeline pipelineName

To find out information on the pipeline command:
$ anadama help pipeline

Demo runs

SixteenS pipeline demo

Follow these steps to run the SixteenS pipeline on a demo data set:

  1. Download the SixteenS demo files
  2. Decompress the SixteenS demo files and then change directories
    • $ tar zxvf 16s_functional_test.tgz
    • $ cd 16s_functional_test
  3. Run the SixteenS pipeline
    • $ anadama pipeline SixteenS -f 'raw_seq_files: Fasting_Example.sff' -f 'sample_metadata: map.txt'

WGS pipeline demo

Follow these steps to run the WGS pipeline on a demo data set:

  1. Download the WGS demo files
  2. Decompress the WGS demo files and then change directories
    • $ tar zxvf wgs_functional_test.tgz
    • $ cd wgs_functional_test
  3. Run the WGS pipeline
    • $ anadama pipeline WGS -f 'raw_seq_files: glob:*.fastq' -o 'decontaminate.threads: 8' -o 'metaphlan2.nproc: 8' -k 'name: humann'