Snakemake 3.7.1 – Scalable Bioinformatics Workflow Engine

Snakemake 3.7.1

:: DESCRIPTION

Snakemake is a workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Snakemake

:: MORE INFORMATION

Citation

Snakemake–a scalable bioinformatics workflow engine.
Köster J, Rahmann S.
Bioinformatics. 2012 Oct 1;28(19):2520-2.

SNPflow 1.3.4 – SNP Workflow Manager

SNPflow 1.3.4

:: DESCRIPTION

SNPflow is a freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

SNPflow

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 SNPflow

:: MORE INFORMATION

Citation

SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.
Weissensteiner H, Haun M, Schönherr S, Neuner M, Forer L, Specht G, Kloss-Brandstätter A, Kronenberg F, Coassin S.
PLoS One. 2013;8(3):e59508. doi: 10.1371/journal.pone.0059508.

RAMPART 0.12.2 – A Workflow Management System for de novo Genome Assembly

RAMPART 0.12.2

:: DESCRIPTION

RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies.

::DEVELOPER

The Genome Analysis Centre (TGAC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RAMPART

:: MORE INFORMATION

Citation

RAMPART: a workflow management system for de novo genome assembly.
Mapleson D, Drou N, Swarbreck D.
Bioinformatics. 2015 Jan 30. pii: btv056.

Jflow 1.1 – A Workflow Management System for Web Applications

Jflow 1.1

:: DESCRIPTION

Jflow is a JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and monitor workflows.

::DEVELOPER

Jflow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript
  • Python

:: DOWNLOAD

 Jflow

:: MORE INFORMATION

Citation

Jflow: a workflow management system for web applications.
Mariette J, Escudié F, Bardou P, Nabihoudine I, Noirot C, Trotard MS, Gaspin C, Klopp C.
Bioinformatics. 2015 Oct 10. pii: btv589

AffyPipe – Pipeline for Affymetrix Axiom Genotyping Workflow

AffyPipe

:: DESCRIPTION

AffyPipe allows you to edit SNP probe classes directly while exporting genotypes in PLINK format

::DEVELOPER

AffyPipe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Python

:: DOWNLOAD

 AffyPipe

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 1;30(21):3118-9. doi: 10.1093/bioinformatics/btu486.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.
Nicolazzi EL, Iamartino D, Williams JL

draw+sneakpeek 201308 – DNA Resequencing Analysis Workflow

draw+sneakpeek 201308

:: DESCRIPTION

DRAW and SneakPeek are two computer programs that we use for analyzing whole-genome and whole-exome DNA-seq experiments.

DRAW stands for DNA Resequencing Analysis Workflow. DRAW automates the entire process of mapping sequence reads, various quality control steps and calling variants.

SneakPeek is a web-based diagnostic tool for reviewing quality metrics generated by our DNA Resequencing Analysis Workflow (DRAW).

::DEVELOPER

 Wang Lab @ IBI

:: SCREENSHOTS

SneakPeek

:: REQUIREMENTS

  • Amazon EC2 / Linux

:: DOWNLOAD

 draw+sneakpeek

:: MORE INFORMATION

Citation

Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, and Wang LS.
DRAW+SneakPeek: Analysis Workflow and Quality Metric Man-agement for DNA-Seq Experiments.
Bioinformatics (2013) 29 (19): 2498-2500. doi: 10.1093/bioinformatics/btt422

LONI Pipeline 5.9.1 – Free Workflow Application

LONI Pipeline 5.9.1

:: DESCRIPTION

The LONI Pipeline is a free workflow application primarily aimed at computational scientists. With the LONI Pipeline, users can quickly create workflows that take advantage of all the greatest tools available in neuroimaging, genomics, bioinformatics, etc.

::DEVELOPER

Laboratory of Neuro Imaging

:: SCREENSHOTS

LONI

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • JRE

:: DOWNLOAD

 LONI Pipeline

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 26;12:304. doi: 10.1186/1471-2105-12-304.
Applications of the pipeline environment for visual informatics and genomics computations.
Dinov ID1, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW.

ballaxy – Galaxy-based workflow toolkit for Structural Bioinformatics

ballaxy

:: DESCRIPTION

ballaxy is a workflow framework for structure based computational biology based on the Galaxy workflow engine.

::DEVELOPER

BALL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Web Server
  • C++ Comipiler

:: DOWNLOAD

 ballaxy

:: MORE INFORMATION

Citation:

ballaxy: web services for structural bioinformatics.
Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.
Bioinformatics. 2014 Sep 2. pii: btu574.

Taverna 2.5 – Workflow Management System

Taverna 2.5

:: DESCRIPTION

Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community.

::DEVELOPER

Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Taverna ; PlugInsAssociated tools

:: MORE INFORMATION

Citation:

D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. Pocock, P. Li, and T. Oinn,
Taverna: a tool for building and running workflows of services.,”
Nucleic Acids Research, vol. 34, iss. Web Server issue, pp. 729-732, 2006.

T. Oinn, M. Greenwood, M. Addis, N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M. Pocock, M. Senger, R. Stevens, A. Wipat, and C. Wroe,
Taverna: lessons in creating a workflow environment for the life sciences,
Concurrency and Computation: Practice and Experience, vol. 18, iss. 10, pp. 1067-1100, 2006.

XiP 3.0 – Construction of Workflows

XiP 3.0

:: DESCRIPTION

XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run,construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

XiP

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 XiP

:: MORE INFORMATION

Citation

Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S.
XiP: a computational environment to create, extend and share workflows.
Bioinformatics. 2013 Jan 1;29(1):137-9