Downloads
v2.5.0.4v2.5.0.4 mirror
*** mrsFAST-Ultra (BETA) NEW ***
All Versions
Quick links
ManualBug Reports
Developers
Can AlkanFaraz Hach
Farhad Hormozdiari
Fereydoun Hormozdiari
Publications
Nature Methods 2010Related Projects
mrFASTdrFAST
SCALCE
mrCaNaVaR
VariationHunter
Resources
Computational Biology Lab, Simon Fraser UniversityEichler Lab, University of Washington
Alkan Lab, Bilkent University
Introduction
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)
News
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 2.5.0.4.
- Bug regarding quality end null characters is fixed.
2012-08-18: mrsFAST version 2.4.0.4 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 2.3.0.2 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 2.0.0.0 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 1.2.6.4 release:
- Bug in reporting a location twice for some reads is fixed.
2009-07-31: mrsFAST version 1.2.6.3 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 1.1.6.2 release:
<li> Performance improvement.
2009-06-04: mrsFAST version 1.1.6.1 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 1.0.6.0 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.
2009-04-28:
- We moved to sourceforge.net.
2009-04-15: mrsFAST version 0.5.1 release:
- Bug Fix: Length of the input file increased.
2009-04-13:
- 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.