Snakemake--a scalable bioinformatics workflow engine.

SUMMARY Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. AVAILABILITY http://snakemake.googlecode.com. CONTACT johannes.koester@uni-due.de.

[1]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[2]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[3]  Tao Xu,et al.  Pegasys: software for executing and integrating analyses of biological sequences , 2004, BMC Bioinformatics.

[4]  Osamu Tatebe,et al.  Pwrake: a parallel and distributed flexible workflow management tool for wide-area data intensive computing , 2010, HPDC '10.

[5]  Bernard J. Pope,et al.  Bpipe: a tool for running and managing bioinformatics pipelines , 2012, Bioinform..

[6]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[7]  Jun'ichi Tsujii,et al.  Design and Implementation of GXP Make -- A Workflow System Based on Make , 2010, 2010 IEEE Sixth International Conference on e-Science.

[8]  Leo Goodstadt,et al.  Ruffus: a lightweight Python library for computational pipelines , 2010, Bioinform..

[9]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[10]  Florian Halbritter,et al.  GeneProf: analysis of high-throughput sequencing experiments , 2011, Nature Methods.

[11]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

[12]  Richard M. Stallman,et al.  GNU make : a program for directing recompilation , 1996 .

[13]  Shawn Hoon,et al.  Biopipe: a flexible framework for protocol-based bioinformatics analysis. , 2003, Genome research.

[14]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[15]  Emden R. Gansner,et al.  An open graph visualization system and its applications to software engineering , 2000 .