Nephele Pipeline Scripts
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Pipes
README.md update readme and config_default Jul 13, 2017

README.md

Nephele Project

Nephele is a cloud-based platform for simplified, standardized, and reproducible microbiome analysis, available at https://nephele.niaid.nih.gov. Nephele intends to allow non-expert bioinformatic users to process microbiome datasets through pipelines of existing software tools. Typically this type of work is computationally intensive and requires knowledge of both scripting and the tools themselves. Nephele attempts to overcome these issues.

To address the computationally intensive aspect, we provision dedicated, cloud-based compute resources, in an on-demand nature, and with an appropriate environment for analyzing user-supplied data. When an analysis pipeline completes, this compute resource is torn down. This means users can process as many datasets as they choose, simultaneously, by machines that are dynamically spun up and shut down.

To ease the learning curve of installing, configuring, and running the software, we stitch together a series of computational tasks into a number of prepared generic pipelines. Pipelines are configured using inputs from simple web-front-end forms, which allow users to specify commonly-changed parameters. We combine these with sensible default parameters, when appropriate.

It is important to note that all of the software which comprises Nephele--for example mothur, QIIME, bioBakery, and a5-miseq--is freely available for use. We do not attempt to supersede or act as a replacement for these component software packages, nor do we modify them. Nephele instead attempts to take a number of useful tools and make them available to a wider audience. We recommend visiting the software creators' websites (listed in the Attribution section below) for details of their implementation.

Nephele has been developed and is maintained by a team from the Office of Cyber Infrastructure and Computational Biology (OCICB), which is part of the National Institute of Allergy and Infectious Diseases (NIAID).

About this repository

The purpose of this repository is to allow Nephele users and others interested in microbiome analysis to examine how we use various software tools within the Nephele platform. This repository contains the pipeline scripts that Nepehele executes on the Amazon cloud to process microbiome sequence data inputs provided by users through Nephele's web interface. The pipeline source code in this repository corresponds to Nephele release version 1.8.

Nephele's pipelines have been collated from a number of sources, and all are being actively worked on. It is important to understand that these pipelines, in their current state, cannot easily be ported to another system and run. They're configured to run when called by other components of Nephele, but can--with a little effort--work in isolation. Please see the usage example in the 'Pipes' directory. We assume that anyone wanting to try this may have questions (e.g., about use of the Amazon Machine Image that contains required libraries and dependencies for the pipelines), and we are happy to address these types of questions and requests via the Issues tracker.

Nephele currently uses Amazon's EC2 platform as a compute resource with curated machine images. We use Amazon's S3 service to store pipeline results for a period of time. A high-level architecture of how Nephele uses various AWS components can be found here.

We would like to thank all contributors to this project, and we are grateful for any and all feedback.

Public Domain license

This is free and unencumbered software released into the public domain.
Be kind, and provide attribution when you use this code.

United States government creative works, including writing, images, and computer code, are usually prepared by officers or employees of the United States government as part of their official duties. A government work is generally not subject to copyright in the United States and there is generally no copyright restriction on reproduction, derivative works, distribution, performance, or display of a government work. Unless the work falls under an exception, anyone may, without restriction under U.S. copyright laws:

  • Reproduce the work in print or digital form
  • Create derivative works
  • Perform the work publicly
  • Display the work
  • Distribute copies or digitally transfer the work to the public by sale or other transfer of ownership, or by rental, lease, or lending

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Learn more about how copyright applies to U.S. government works at USA.gov

Attribution for Third-Party Software

The following open-source software packages are in use within Nephele's pipelines. Citations for each package are also listed. Please be aware that these packages generally use or require other open-source software packages, and those licenses are listed on the individual software applications' websites.


mothur (GPLv3; https://www.mothur.org/) Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537-41.

QIIME (GPLv2; http://qiime.org/) Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez Pena A, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 2010;7(5):335-336.,

QIIME uses multiple open source software tools that should also be cited. Please see "Citing QIIME" on the above link for details.

biobakery (various open-source licenses; https://bitbucket.org/biobakery/biobakery/wiki/Home) Huttenhower C. Huttenhower Lab Tools [Internet]. Cambridge (MA): The Huttenhower Lab Department of Biostatistics, Harvard T.H. Chan School of Public Health; 2015 July 15 [cited 2015 Sep 16]. Available from https://bitbucket.org/biobakery/biobakery/wiki/Home

A5-miseq (GPLv3; https://sourceforge.net/projects/ngopt/) Coil D, Jospin G, Darling AE. A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31(4):587-589.