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Converts SOLID XSQ/HDF files to fastq or csfasta files.
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The XSQConverter tool converts SOLiD XSQ files to normal Sanger colorspace fastq or to BWA 0.5.9 specific (double encoded) colorspace fastq files. There is also an option to output CSFasta and qual 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 some java code written by myself to process the XSQ file.

The output is a directory structure with output files in the specified format for every combination of library(lib_sample1, lib_sample2) and tag (F3, F5 ,R3 etc).

I have added a zip file with the HDF5 native c++ libraries and the java wrappers to the source because I have had troubles myself downloading the correct libraries again from the HDFGroup website.
The libraries are from

Other libraries used are from apache commons and a junit-addon.

More information about the XSQ format is here:

The command line interface:

usage: XSQ converter version v10:03-07-2013 . By default converts all XSQ libraries into CSFastQ files except the Unassigned_* and the Unclassified library. Options -i and -o are required.

-b,--barcode barcodes which should be converted. For multiple barcodes use this argument multiple times

-c,--chunk output fastq chunksize. Default is 1000000

-d,--display display all libraries names and quit without processing

-f,--fastq-dialect fastQ dialect / format. Either BWA, Sanger or csfasta.

-h,--help print this message

-i,--input XSQ input file path.

-j,--javapath display Java path

-l,--library library which should be converted. For multiple libraries use this argument multiple times

-m,--matepair-barcode-file file with matepair bacodes. Each line should contains a barcode color space sequence and a barcode name, separated with a tab. All barcodes are required to have the same length. A output file is created for every barcode name and tag combination.

-mpbl The location of the matepair barcode sequence. Either F3 or R3. Default is F3

-n,--matepair-barcode-mismatches number of mismatches to be allowed for matching matepair barcodes. Default is 0.

-o,--output output directory path

-t Add the leading base and color call. BWA and Bowtie do not use these but other mappers do. Not yet available for mate pair barcode runs. Can only be used for output in Sanger or csfasta format.

-u,--use-barcode-name use barcode in the output names. Should always be used when processing multiple unassigned libraries by barcode because they have the same name.

-w,--overwrite overwrite existing output. By default libraries for which existing output is present are skipped.

-x,--read-lenght-cutoff Only output reads untill this cutoff. Works on all tags.

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