Building and documenting workflows with python-based snakemake

German Conference on Bioinformatics 2012, GCB 2012

Volumn , Issue , 2012, Pages 49-56

  Köster, Johannes ^a,b   Rahmann, Sven ^a  

^a UNIVERSITY OF DUISBURG ESSEN   (Germany)

^b UNIVERSITY HOSPITAL ESSEN   (Germany)

Author keywords

Dependency graph; Highthroughput sequencing; Knapsack problem; Next generation sequencing; Python; Workflow engine

Indexed keywords

DEPENDENCY GRAPHS; HIGH-THROUGHPUT; KNAPSACK PROBLEMS; NEXT-GENERATION SEQUENCING; PYTHON; WORKFLOW ENGINES;

BIOINFORMATICS;

HIGH LEVEL LANGUAGES;

EID: 84871190031     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.4230/OASIcs.GCB.2012.49     Document Type: Conference Paper

References (15)

1. Emden R. Gansner and Stephen C. North. An open graph visualization system and its applications to software engineering. Software-Practice and Experience, 30(11):1203-1233, 2000.
2. Jeremy Goecks, Anton Nekrutenko, James Taylor, and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8):R86, 2010.
3. Leo Goodstadt. Ruffus: A lightweight python library for computational pipelines. Bioinformatics, 26(21):2778-2779, November 2010.
4. Florian Halbritter, Harsh J. Vaidya, and Simon R. Tomlinson. GeneProf: analysis of highthroughput sequencing experiments. Nature Methods, 9(1):7-8, December 2011.
5. Shawn Hoon, Kiran Kumar Ratnapu, Jer-Ming Chia, Balamurugan Kumarasamy, Xiao Juguang, Michele Clamp, Arne Stabenau, Simon Potter, Laura Clarke, and Elia Stupka. Biopipe: A flexible framework for Protocol-Based bioinformatics analysis. Genome Research, 13(8):1904-1915, August 2003.
6. J.D. Hunter. Matplotlib: A 2D graphics environment. Computing in Science Engineering, 9(3):90-95, June 2007.
7. Heng Li and Richard Durbin. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14):1754-1760, July 2009.
8. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, and Richard Durbin. The sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16):2078-2079, August 2009.
9. Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly, and Mark A. DePristo. The genome analysis toolkit: A MapReduce framework for analyzing Next-Generation DNA sequencing data. Genome Research, 20(9):1297-1303, September 2010.
10. Matthew Meyerson, Stacey Gabriel, and Gad Getz. Advances in understanding cancer genomes through second-generation sequencing. Nature Reviews Genetics, 11(10):685-696, September 2010.
11. Tom Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, Mark Greenwood, Tim Carver, Kevin Glover, Matthew R Pocock, Anil Wipat, and Peter Li. Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 20(17):3045-3054, November 2004.
12. Simon P Sadedin, Bernard Pope, and Alicia Oshlack. Bpipe: A tool for running and managing bioinformatics pipelines. Bioinformatics, April 2012.
13. Richard M. Stallman and Roland McGrath. GNU Make-A Program for Directing Recompilation. 1991.
14. Masahiro Tanaka and Osamu Tatebe. Pwrake: a parallel and distributed flexible workflow management tool for wide-area data intensive computing. In Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, HPDC '10, page 356-359, New York, NY, USA, 2010. ACM.
15. K. Taura, T. Matsuzaki, M. Miwa, Y. Kamoshida, D. Yokoyama, N. Dun, T. Shibata, C. S Jun, and J. Tsujii. Design and implementation of GXP make-a workflow system based on make. Future Generation Computer Systems, 2011.