What it does

Runs the CLCbio tool clc_mapper which produces a proprietary binary CAS format file, which is immediately processed using clc_cas_to_sam to generate a self-contained standard BAM file, which is then sorted and indexed using samtools.

Citation

If you use this Galaxy tool in work leading to a scientific publication please cite this wrapper as:

Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell

CLC Assembly Cell, CLC bio (2008--2015) https://www.qiagenbioinformatics.com/products/clc-assembly-cell/

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell