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 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.
This project provides the following mailing lists.
- solid_xsq_converter-users: a list intended for general discussion on the project.
- solid_xsq_converter-commits: a list that receives source code commit messages.
- solid_xsq_converter-devel: a list intended for discussion among developers (subscription is restricted to registered developers).
Compiled program with HDF5 java libraries
HDF5 native C++ libraries (are used by the java libraries, put them somewhere on the javaPath
Only the HDF5 libraries
All the HDF5 libraries can also be found on Java page of the HDF group http://www.hdfgroup.org/hdf-java-html/
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.
- TracGuide -- Built-in Documentation
- TitleIndex -- A complete list of local wiki pages.
- Trac FAQ -- Frequently Asked Questions
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