Previous Versions Git
mrsFAST-Ultra Manual (v >= 3.0.0)
mrsFAST Manual (v <= 220.127.116.11)
Nucleic Acid Research 2014
Nature Methods 2010
Computational Biology Lab, Simon Fraser University
Eichler Lab, University of Washington
Alkan Lab, Bilkent University
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:
- Mistmatches, No indels
- Paired-end Mapping Mode
- Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
git clone git://git.code.sf.net/p/mrsfast/code mrsfast
- 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
- 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
- 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
- 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
- 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
- Bug Fixes related to optional fields
- Bug Fixes related to mrsfast crash in PE mode.
- git repo is now available
- Bug Fix: #28 in discordant-vh mode
- new target for make file. with-sse4
- 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 relase
- Source code of mrsFAST-Ultra is released.
2013-07-23: mrsFAST version 18.104.22.168 relase
- 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-beta relase
- Bug Fixes.
- Manaul can be found mrsFAST-Ultra Manual.
- 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 22.214.171.124.
- Bug regarding quality end null characters is fixed.
2012-08-18: mrsFAST version 126.96.36.199 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 188.8.131.52 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.
- 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 184.108.40.206 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 v220.127.116.11 for Bisulfite mapping until it is implemented in cache oblivious version
2009-09-11: mrsFAST version 18.104.22.168 release:
- Bug in reporting a location twice for some reads is fixed.
2009-07-31: mrsFAST version 22.214.171.124 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 126.96.36.199 release:
<li> Performance improvement.
2009-06-04: mrsFAST version 188.8.131.52 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 184.108.40.206 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.
- We moved to sourceforge.net.
2009-04-15: mrsFAST version 0.5.1 release:
- Bug Fix: Length of the input file increased.
- mrsFAST's Manual is available now.
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.