BigDataScript: A scripting language for data pipelines

Bioinformatics

Volumn 31, Issue 1, 2015, Pages 10-16

  Cingolani, Pablo ^a   Sladek, Rob ^a   Blanchette, Mathieu ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; WORKFLOW;

COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROGRAMMING LANGUAGES; SOFTWARE; WORKFLOW;

EID: 84922388906     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu595     Document Type: Article

References (13)

1. Auwera,G.A. et al. (2013) From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinformatics, 11.10. 11-11.10. 33.
2. Cingolani,P. et al. (2012a) Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Frontiers in genetics, 3, 35.
3. Cingolani,P. et al. (2012b) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6, 80-92.
4. Feldman,S.I. (1979) Make-A program for maintaining computer program. Software, 9, 255-265.
5. Goodstadt,L. (2010) Ruffus: a lightweight python library for computational pipelines. Bioinformatics, 26, 2778-2779.
6. Kc oster,J. and Rahmann,S. (2012) Snakemake-A scalable bioinformatics workflow engine. Bioinformatics, 28, 2520-2522.
7. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics, 25, 1754-1760.
8. McKenna,A. et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
9. Napolitano,F. et al. (2013) Bioinformatic pipelines in Python with Leaf. BMC Bioinformatics, 14, 201.
10. Parr,T. (2007) The Definitive ANTLR Reference: Building Domain-specific Languages. Pragmatic Bookshelf Raleigh, NC.
11. Reynolds,J.C. (1993) The discoveries of continuations. LISP Symbol. Comput., 6, 233-247.
12. Sadedin,S.P. et al. (2012) Bpipe: a tool for running and managing bioinformatics pipelines. Bioinformatics, 28, 1525-1526.
13. Zuk,O. et al. (2014) Searching for missing heritability: designing rare variant association studies, Proc. Natl Acad. Sci.s, 111, E455-E464.