QDNAseq Galaxy tool
====================

This galaxy-tool is a wrapper for the R Bioconductor package [QDNAseq]

It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.

For questions/remarks about the bioconductor package itself, see also the code at [github].

[QDNAseq]: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
[github]: https://github.com/ccagc/QDNAseq


Installation
---------------------

This tool should be installed into a galaxy installation from the (test)toolshed (tool-name: qdnaseq).


Sample workflow
---------------------

You can test this tool at a galaxy installation by using built-in data by selecting the option "Run with test data" and press execute.


Citation
---------------------

For the underlying QDNAseq R package please cite: 
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B (2014). “DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.” Genome Research. doi:10.1101/gr.175141.114.

See also the bioconductor package [documentation].

[documentation]: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html

