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Welcome to project Solid_XSQ_converter

The Solid_XSQ_converter tool converts Solid XSQ files to normal Sanger CS fastq or to BWA 0.5.9 specific CS fastq dialect files.

This tool is able to convert XSQ files comparatively fast by using the native HDF5 C++ libraries, OO wrapped by HDF5 Java library plus a minimal amount of java code written by myself to process the XSQ file.

Quality Assurance

Quality of the output has been checked by diffing the CSFastQ output from this tool to the CSFastQ output of other tools. Please still compare the output of this tool to the output of your previous conversion tool to make sure the output is also correct in your environment / setup. A few Linux command to do this are provided in a text document on the download page.

Developed by Wim Spee from the Hubrecht Cuppen group.

Contact:

w[dot]spee[AT]hubrecht[dot]eu

w.spee@…

Mailing lists

This project provides the following mailing lists.

Compiled program with HDF5 java libraries

https://trac.nbic.nl/solid_xsq_converter/downloads

HDF5 native C++ libraries (are used by the java libraries, put them somewhere on the javaPath

https://trac.nbic.nl/solid_xsq_converter/downloads

Only the HDF5 libraries

https://trac.nbic.nl/solid_xsq_converter/downloads

All the HDF5 libraries can also be found on Java page of the HDF group http://www.hdfgroup.org/hdf-java-html/

Source access

If available, anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/solid_xsq_converter solid_xsq_converter

Write access is only available to registered developers.

You can become a developer by registering yourself if you haven't already done so, and requesting write access on the solid_xsq_converter-users mailing list.

Starting Points

Other NBIC software projects

All active NBIC software projects can be accessed from the project index.

Last modified 5 years ago Last modified on Aug 16, 2012, 9:22:39 AM