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Copyright and installation instructions are contained within the package. We strongly recommend that you consult the tutorial before attempting to use SpliceMap.

The latest version of Bowtie is included in the binaries for your convienience. Bowtie is developed by Ben Langmead and details can be found on his website. We include Bowtie since there is no guarentee that any newer or older version will be compatible.

SpliceMap (Linux-x86 64bit) This is the recommended version for everyone. Please see the release notes for more information
SpliceMap (Linux-x86 32bit) This is the 32-bit version, if your system requres it.
SpliceMap (OSX 64bit) This is the Mac OSX (intel-64 bit) version.
SpliceMap 2.1.1 (Linux) This older version is no longer supported. Only supports 50bp reads. Still avaliable as this will produce identical output to the results on the paper.

Older versions in Python are also provided for historical purposes.

SpliceMap 3.0 (Python) This is an older release written in Python.
SpliceMap 2.0 (Python) This is an older release written in Python.

SpliceMap - Release Notes

This release fixes a bug regarding multi-hits.

  • (another) Multi-hit bug fix

SpliceMap - Release Notes

This release fixes a bug regarding multi-hits and has some new features.

  • Multi-hit bug fix
  • New option "max_multi_hit" specifies the maximum number of multi-hits allowed in the seeding (not the full reads).
  • Small formatting issue in SAM/coveraege file fixed

SpliceMap 3.3.5 - Release Notes

This release has a large part re-implemented for increased reliability and speed. There are also new options to improve the alignment. Future versions will focus on improving the alignment sensitivity by rescuing some pair reads. In the next point release we will try to associate junctions with an annotated gene name.

  • Able to set the number of maximum number of mismatches in each read
  • SAM output shows the number of mismatches in each read
  • SAM output shows where the mismatches lie
  • SAM output shows the number of soft clipped bases in each read
  • Able to set the number of maximum number of bases clipped in each read
  • SAM output shows the number multiple hits of each read
  • SAM output indicates the inferred insert size
  • SAM output correctly indicates if a pair is not mapped
  • Memory usage much less dependent on total number of reads
  • Non-unique coverage outputted by default, this is no longer an option and requires no extra memory
  • Includes latest version of Bowtie (0.12.7)

SpliceMap - Release Notes

This release reduces the memory requirement significantly for large datasets, improves stability and introduces some new features. The next version will further reduce memory consumption.

SpliceMap - Release Notes

This release fixed a bug in the SAM file output of quality scores.

SpliceMap 3.3.3 - Release Notes

SpliceMap 3.3.3 bring a number of new features. Most notable is the support for uneven read lengths in both pairs. For example, if reads in your pairs range from [50-73bp] due to trimming, SpliceMap will happily align them. Upcomming features in future releases include a "NM" tag for each read in the SAM file, support for concatentated genome files and options for extra specificity from long reads. The changes in 3.3.3 are listed below:

SpliceMap - Release Notes

SpliceMap fixes the single-read bug.

SpliceMap - Release Notes

SpliceMap fixes some bugs and adresses compatibility issues. If you have an older system and had problems running previous version of SpliceMap, this version might help. SAMtools now works properly with the SAM output.

SpliceMap 3.3.1 - Release Notes

SpliceMap 3.3.1 is a bug fix release. There were some problems with the new wild-card expression for chromosome files so we have reverted to the old one and added an option in the .cfg file.

SpliceMap 3.3 - Release Notes

SpliceMap 3.3 changes the algorithm handling long reads, bringing much better sensitivity.

SpliceMap 3.2.2 - Release Notes

SpliceMap 3.2.2 is another minor release, it fixes some issues people had with compiling on the latest version of g++ (4.4.3)

SpliceMap 3.2.1 - Release Notes

SpliceMap 3.2.1 fixes some minor problems. If you are not currently experiencing issues you can skip this release.

SpliceMap 3.2 - Release Notes

SpliceMap 3.2 adds Bowtie support and changes the command line inputs to a configuration file.

SpliceMap 3.1.1 - Release Notes

SpliceMap 3.1.1 brings some major internal changes to SpliceMap. Most notably are SAM support and faster speed. Other changes are

SpliceMap 2.1.1 - Release Notes

This version only supports 50bp length reads and is no longer supported. It remains due to historical reasons.