Micro-read substitution-only Fast Alignment Search Tool


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
  • Multi-threading

Legacy Bisulfite Mapping Mode (see version 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- 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.


Feel free to send your inquiries to @isarrafi or @fhach.

Bug Reports

To report any bugs or issues please refer to the issues page.


mrsFAST-Ultra is brought to you by:

From the Lab for Computational Biology at Simon Fraser University, Eicher Lab at University of Washington, and Alkan Lab at Bilkent University.

Release Notes

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 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

2012-11-16: mrsFAST version release:

  • Bug regarding quality end null characters is fixed.

2012-08-18: mrsFAST version 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 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 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 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 v1.2.6.4 for Bisulfite mapping until it is implemented in cache oblivious version

2009-09-11: mrsFAST version release:

  • Bug in reporting a location twice for some reads is fixed.

2009-07-31: mrsFAST version 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 release:

  • Performance improvement.

2009-06-04: mrsFAST version 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 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.