SpliceMap

  • SpliceMap is a de novo splice junction discovery
    and alignment tool. It offers high sensitivity and support
    for arbitrary RNA-seq read lengths.
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Latest News: SpliceMap 3.3.5.2 -- Faster and more accurate ... read more

Getting Started

These simple steps will help you integrate SpliceMap into your transcriptomics analysis pipeline.

Publication

Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, and Wing Hung Wong
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Nucleic Acids Research, Advance access published on April 5, 2010. [preprint]

Latest News

10-23-2010: SpliceMap 3.3.5.2 Released

This release fixes a bug regarding multi-hits.

10-1-2010: SpliceMap 3.3.5.1 Released

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

9-20-2010: SpliceMap 3.3.5 Released

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.

9-5-2010: SpliceMap 3.3.3.2 Released

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.

8-23-2010: Memory usage issue

Note that SpliceMap 3.3.3.1 uses over 50GB for 200 million reads. In the next version we will reduce this requirement significantly.

8-19-2010: SpliceMap 3.3.3.1 Released

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

8-18-2010: SpliceMap 3.3.3 Released

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. Upcoming features in future releases include a "NM" tag for each read in the SAM file, support for concatenated genome files and options for extra specificity from long reads. The changes in 3.3.3 are listed below:

7-6-2010: SpliceMap 3.3.1.3 Released -- Single-read bug fixed

SpliceMap 3.3.1.3 fixes the single-read bug. Now, you may use single-read data just like pair-reads. The next update of SpliceMap will be quite significant (so may take a while).

7-2-2010: Single-read bug

There has been a bug discovered regarding the use of single-reads. When the new code was added for improved long pair-reads, it was not updated for single-reads by me (John Mu). Very sorry about that! There have been a number of problems as a result of this for people who use single-reads, including not discovering many junctions.

A fixed version will be out in a few days, with an announcement.

Please note: If you use pair-reads, there is nothing to be worried about. It is fine.

6-30-2010: SpliceMap 3.3.1.2 Released

SpliceMap 3.3.1.2 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.

6-17-2010: SpliceMap 3.3.1 Released

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.

For detailed information about this release, please see the release notes.

6-14-2010: SpliceMap 3.3 Released

SpliceMap 3.3 brings major improvements to sensitivity when aligning longer reads. The 3.3.x strain will next add more reliable handling of file formats as well as handling of read quality. In future versions we will add an option to use the extra information in the long reads to improve specificity rather than sensitivity.

For detailed information about this release, please see the release notes.

6-5-2010: SpliceMap 3.2.2 Released

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). The next version will include some fixes to improve sensitivity with long reads (100bp+).

For detailed information about this release, please see the release notes.

6-1-2010: SpliceMap 3.2.1 Released

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

For detailed information about this release, please see the release notes.

5-31-2010: SpliceMap 3.2 Released

SpliceMap 3.2 includes Bowtie support and usability improvements. The next version will continue to add support for more read formats and mappers. Major changes for this version include:

For detailed information about this release, please see the release notes.

5-18-2010: SpliceMap 3.1.1 Released

SpliceMap 3.1.1 brings SAM output support and many general improvements. The next version will add support for more read mappers such as Bowtie and BWA. Major changes for this version include: For detailed information about this release, please see the release notes.

5-15-2010: New Website!

The website has been completely redesigned for easy navigation. A new tutorial and getting started guide is included for your convenience.