Converts XSQ format files to FASTQ format files.
Requires the pytables library and HDF5-devel libraries to be installed. (Note: pytables also requires numpy, numexpr, and cython)
HDF5 libraries can be downloaded from http://www.hdfgroup.org/HDF5/. They can also be found in the EPEL yum repository. Pytables requires HDF5 1.6.10 or better.
The installation script install.sh will take care of setting up a virtualenv environment and installing Pytables and it's dependencies. The virtualenv will be setup in the 'env' directory. The default xsq driver script expects this setup and will automatically setup the virtualenv accordingly.
When converting a sample or entire file, multiple processors can be used to speed the conversion.
xsq cmd {opts} filename.xsq
Commands:
info - Lists all of the data associated with the XSQ file
list - Lists the samples and tags (R3/F3/etc) present in the file
Options:
-c Show the number of reads present for each tag
-min {val} Hide samples that have less than {val} reads
convert - Converts XSQ samples and fragments to FASTQ format
Options:
-a Convert all samples (saves to sample_name.fastq.gz)
[-a additional options]
-desc Use descriptions for the sample name
-f Overwrite existing files
-min {val} Skip samples that have less than {val} reads
-noz Don't compress the output FASTQ files with gzip
-fsuf {val} Add suffix to file name
-unclassified Export "Unclassified" library (usually skipped)
-n name Convert only sample "name" (writes to stdout)
(can be only one, written uncompressed)
-procs {val} Use {val} number of threads (CPUs) to convert one
region at a time. (default 1)
-s suffix Append a suffix to all read names
-t tag Convert only this tag (can be more than one)
If more than one tag is given, the sequences for
each read will be written out together.
For example:
@read1 F3
F3 seq
+
F3 qual
@read1 R5
R5 seq
+
R5 qual
@read2
...
The default is to convert all samples and all fragments/tags.