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 126.96.36.199 (Linux-x86 64bit)||This is the recommended version for everyone. Please see the release notes for more information|
|SpliceMap 188.8.131.52 (Linux-x86 32bit)||This is the 32-bit version, if your system requres it.|
|SpliceMap 184.108.40.206 (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 220.127.116.11 - Release Notes
This release fixes a bug regarding multi-hits.
- (another) Multi-hit bug fix
SpliceMap 18.104.22.168 - 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 22.214.171.124 - 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.
- Support for almost unlimited number of chromosomes and read files
- Able to read concatenated genome files (you and even mix and match multiple FASTA reference files)
- Checks bowtie index to make sure it is valid
- Able to map 'bad' reads with residual adaptor sequences
- Stability improvements
- Reduced memory consumption
SpliceMap 126.96.36.199 - 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:
- Support for trimmed reads with uneven length
- Option to run multiple chromosomes are the same time (at the cost of memory)
- Read quality is now copied to the SAM file
- Read names are copied to the SAM file
- Option to set "temp" and "output" directories
- Non-unique hits are marked with MAPQ = 0 in the SAM file
- Faster alignment by only mapping unique reads
- Bowtie index is automatically built, if it is not found
- SAM file sorted properly for cufflinks
- Less verbose, output logs redirected to "debug_logs" folder
- More checking of reads/genome
SpliceMap 188.8.131.52 - Release Notes
SpliceMap 184.108.40.206 fixes the single-read bug.
- Also fixed a bug with the display of "max_intron" and "min_intron"
SpliceMap 220.127.116.11 - Release Notes
SpliceMap 18.104.22.168 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.
- Removed trailing tab from the SAM output. If you have existing SAM files and do not want to re-run SpliceMap, simply strip off the last tab character and the file will work with SAMtools.
- Addressed a file handling issue with older version of g++
- Binaries are now compiled by default by an older version of g++ for maximum compatibility. If you have a newer version of linux, I suggest you recompile the binaries with "install.sh" and "install-bowtie.sh" for maximum performance.
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.
- Reverted to using "chr*.fa" to detect chromosome by default.
- Added "chromosome_wildcard" option to the .cfg file for people with chromosome in different formats. eg. if your chromosomes are "chr1.fas", "chr2.fas", etc... Then the wild-card expression should be "chr*.fas".
SpliceMap 3.3 - Release Notes
SpliceMap 3.3 changes the algorithm handling long reads, bringing much better sensitivity.
- 40%+ improved sensitivity when using long reads (100bp+)
- Added a section describing the optional filters. Including addition of neighbor filter.
- Added options in the .cfg file:
- Intron size (max-intron,min-intron)
- clipping of bases from the front (as well as end) of read (full_read_length, head_clip_length)
- Some minor fixes to the SAM output, outputs correct number of I's
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)
- Added required libraries for compiling on g++ 4.4.3
- Made makefile a bit nicer
- Now includes "run.cfg", sorry about that...
- Includes new scripts to help the process of building from source
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.
- Removed requirement of TR1 library. (some people had problems building from source)
- Extra checking of the exsitance of files
SpliceMap 3.2 - Release Notes
SpliceMap 3.2 adds Bowtie support and changes the command line inputs to a configuration file.
- Fixed bug relating the the direction flag in SAM output
- Added Bowtie is new default mapper
- Mac OSX support
- FASTA, FASTQ and RAW read support
- uses .cfg file instead of command-line options. Please see the tutorial for details
- Removed support for running SpliceMap on a single chromosome. However, you can still do this by making your own index for that chromosome.
- SAM file sorting uses less memory
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
- Source code included in package
- Junction Search is 3x faster and uses less memory
- Optional filtering, as outlined in the paper
- Build script
- Merges all chromosomes properly
- More accurate coverage calculation
- Executable name changed to "SpliceMap" from "SpliceMapCC"
- Output stored in separate folder
- Junctions are colored in output
SpliceMap 2.1.1 - Release Notes
This version only supports 50bp length reads and is no longer supported. It remains due to historical reasons.