mrsFAST is designed to map short reads to reference genome assemblies; in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.
Currently Supported Features:
- Mismatches, no indels
- Paired-end Mapping
- Discordant Paired-end Mapping (to be used in conjunction with Variation Hunter)
- Best Mapping
- Limited Mapping
- SNP-aware Mapping
Legacy Bisulfite Mapping Mode (see version 220.127.116.11): This is a legacy version and is not being supported at the moment. We are aware of a small bug in paired-end mode of mrsFAST-18.104.22.168 that causes mrsFAST to lose some of its mapping locations(<2%). This legacy version is not cache oblivious.
To download and use mrsFAST please use the side links.
To report any bugs or issues please refer to the issues page.
mrsFAST-Ultra is brought to you by:
2016-11-16: mrsFAST-Ultra version 3.4.0 release:
- New Feature: –tail-crop is added to crop from tail of the reads.
2016-08-30: mrsFAST-Ultra version 3.3.11 release:
- Bug Fix: Fixing the FLAG in best mapping mode for the case in which OEA’s second mate is reverse complemented.
2016-08-12: mrsFAST-Ultra version 3.3.10 release:
- Bug Fix: Fixing MPOS in second mate of limited mapping mode.
2016-06-29: mrsFAST-Ultra version 3.3.9 release:
- exit(0) and exit(1) replaced by exit(EXIT_SUCCESS) and exit(EXIT_FAILURE), respectively
- opening file failures are not report correct exit codes
- concordant calculations is now reported to concordant.statistic
2015-09-17: mrsFAST-Ultra version 3.3.8 release:
- SNP mode is more flexible and accepts non-homosapien dbSNP (VCF) inputs
- Minor fix in memory allocation
- Typo fixed in manual
2015-03-17: mrsFAST-Ultra version 3.3.7 release:
- Makefile supports parallel make -j
- Bug fix: Seg fault in paired-end mode with compressed input
- Window size input is not allowed in search mode
2014-11-03: mrsFAST-Ultra version 3.3.6 release:
- Bug fix: Incorrect number of mappings reported in paired-end -n mode
- Typo fixed in manual
2014-10-30: mrsFAST-Ultra version 3.3.5 release:
- Bug fix: Segmentation fault in paired-end -n mode
- Typos fixed in manual
- Changes in reverse() and reverseComplete() to avoid potential seg faults
2014-09-23: mrsFAST-Ultra version 3.3.4 release:
- Maximum number of SNPs increased to 6 million per chromosome
- Bug fix: Output buffer overflow in single-end best-mapping mode
2014-09-12: mrsFAST-Ultra version 3.3.3 release:
- Bug fix: snp_indexer invalid path caused seg fault
- Bug fix: SNP mode crashed with more than one set of reads
2014-08-06: mrsFAST-Ultra version 3.3.2 release:
- Bug Fixes related to optional fields
- Bug Fixes related to mrsfast crash in PE mode.
- git repo is now available
2014-03-31: mrsFAST-Ultra version 3.3.1 release:
- Bug Fix: #28 in discordant-vh mode
- new target for make file. with-sse4
2014-01-14: mrsFAST-Ultra version 3.3.0 and Graphical User Interface release:
- A new GUI is released for mrsFAST-ultra.
- Bug Fix: Q-gram calculation for the last character of the reference genome
- Code is ported to OS X Mavericks and is compatible with clang.
2013-09-13: mrsFAST-Ultra version 3.2.0 release:
- Source code of mrsFAST-Ultra is released.
2013-07-23: mrsFAST version 22.214.171.124 release:
- Bug Fix. Thanks to J.K Teer for the patch.
- This is the final release of mrsFAST. We will continue to support mrsFAST-ultra.
2013-06-07: mrsFAST-Ultra version 3.1.0 release:
- Bug Fixes.
- Manaul can be found here.
2013-01-16: mrsFAST-Ultra version 3.0.0 beta release:
- Source code will be released at a later date.
- Please use -h option to see the command line.
- This version requires SSE4 instruction set.
- Disclaimer: This version may contain bugs as it is “beta” release. If you want stable version, please use version 126.96.36.199.
2012-11-16: mrsFAST version 188.8.131.52 release:
- Bug regarding quality end null characters is fixed.
2012-08-18: mrsFAST version 184.108.40.206 release:
- Phread offset is added
- Option DISCORDANT_CUT_OFF is added
- Bug regarding MD field is fixed.
- Bug regarding CIGAR field is fixed.
- Output format is changed to reflect the changes in ““VariationHunter””.
2010-05-03: mrsFAST version 220.127.116.11 release:
- Quality field for fasta file in sam ouput is corrected.
- Window size issues are fixed.
- Path related issues are fixed.
- Comments in fasta/fastq formats are ignored.
2010-02-08: mrsFAST version 18.104.22.168 release:
- Bug fixed with respect to flag field of sam output
- Bug fixed with respect to file path in discordant-vh and paired end mode
- –min and –max are now defining the inferred size between mates (distance between outer edges of the mappings mates)
2009-12-08: mrsFAST version 22.214.171.124 release:
- New cache oblivious algorithm, it is now 2x faster in comparison to its predecessor.
- Supports Single end, Paired-end and Discordant Paired-end Mappings modes
- Bugs fixed with respect to paired-end mapping mode
- We are keeping v126.96.36.199 for Bisulfite mapping until it is implemented in cache oblivious version
2009-09-11: mrsFAST version 188.8.131.52 release:
- Bug in reporting a location twice for some reads is fixed.
2009-07-31: mrsFAST version 184.108.40.206 release:
- Bugs #2828635 and #2828636 are fixed.
- Bugs in paired end mode are fixed.
- SAM fields ISIZE is fixed.
- –crop is added to command line options.
2009-06-17: mrsFAST version 220.127.116.11 release:
- Performance improvement.
2009-06-04: mrsFAST version 18.104.22.168 release:
- Paired-end reads in two files with the same name (and without identifiers /1, /2) are supported.
- SAM fields MD and CIGAR are implemented.
- mrsFAST screen output is modified
2009-06-01: mrsFAST version 22.214.171.124 release:
- Command Line Options are simplified.
- Sequences can be read from gz files.
- Mapping output can be reported into gz files.
- Mapping outputs are reported in SAM format.
- Memory usage is reported in the output.
- Bugs related to index phase are fixed.
2009-04-15: mrsFAST version 0.5.1 release:
- Bug Fix: Length of the input file increased.
2009-04-13: mrsFAST version 0.5 release:
- Bisulfite Mapping for pair-end reads is added.
2009-04-06: mrsFAST version 0.4 release:
- Bisulfite Mapping Mode is added for single reads.
- Two file input for Pair-end reads are supported
2009-03-31: mrsFAST version 0.2.1 release:
- Memory leakage during indexing is fixed.
- Memory leakage during loading reads is fixed.
2009-03-30: mrsFAST version 0.2 release:
- Pair-end mapping mode is added.
- A reserved byte is added to Index file.
2009-03-25: mrsFAST version 0.1 release:
- Command Line Mode execution is added.
- Index file size is reduced.
- Both Fasta and Fastq formats are supported.