Fast Alignment Search Tool suite (original) (raw)

mrFAST & mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.

• mrFAST: micro-read Fast Alignment Search Tool.
  Currently Supported Features:
  • Output in SAM format
  • Indels up to 8 bp (4 bp deletions and 4 bp insertions)
  • Paired-end mapping
    • Discordant option to generate mapping file ready for VariationHunter to detect structural variants.
  • One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq
  • Matepair library mapping (long inserts with RF orientation).
    Planned Features:
  • Multithreading

Important notice for mrFAST users: mrFAST with FastHASH (post 2.5.0.0) is drastically faster than plain mrFAST (pre 2.5.0.0). When using mrFAST, please ensure the version is > 2.5.0.0.

mrFAST project moved to GitHub.

This page is kept for reference purposes only.

2014-10-27: mrFAST version 2.6.1.0 release:

• Bug in edit distance calculation for when -e is set to two is fixed.
• Reduction in code. Unnecessary and unused functions removed.
• Minor compilation warnings fixed.

2014-07-10: mrFAST version 2.6.0.2 release:

• Minor bug fixes.
• Memory usage is reduced.

2013-04-01: mrFAST version 2.6.0.1 release:

• Full compliance with the Intel C Compiler, provided by Benoît Leveugle and Laurent Manchon.

2013-01-14: mrFAST version 2.6.0.0 release:

• Memory leak introduced in 2.5.1.1 is fixed.
• New virtual long k-mers to improve speed for high edit distance values.

2013-01-03: mrFAST version 2.5.1.1 release:

• Bug regarding long chromosome names win single end best mode is fixed.

2012-12-27: mrFAST version 2.5.1.0 release:

• Speed improvement in single end mode.

2012-11-30: mrFAST version 2.5.0.4 release:

• Bug regarding CIGAR strings is fixed.
• Allowance for longest chromosome length is increased to 330Mb.

2012-11-28: mrFAST version 2.5.0.3 release:

• Bug regarding quality end null characters is fixed.
• Bug regarding long read names is fixed.

2012-11-14: mrFAST version 2.5.0.2 release:

• Bug causing mrFAST to freeze in paired-end mode for certain inputs is fixed.

2012-11-02: mrFAST version 2.5.0.1 release:

• Minor bug that missed alignments at the edges of contigs is fixed.
• Incorrect SAM header fields are fixed

2012-08-10: mrFAST version 2.5.0.0 release:

• New FastHASH algorithm to accelerate mrFAST by several fold, depending on the read length and error distance cutoff.
  • We strongly suggest rebuilding genome indices to take advantage of FastHASH.
• Matepair library mapping support through --mp parameter
• Mapping quality (MAPQ) is now supported for paired-end mapping, and when the "--best" option is selected in single-end mapping mode.
• Several bugfixes regarding sensitivity and I/O.
• Mapping counters are now shown in paired-end mapping mode.
• DIVET score calculation is fixed.
• DIVET format is slightly changed to fit the requirements of the latest version of VariationHunter.
• When the .fai file (fasta index as created by samtools) is available, the header is now added to the SAM output.
  • Additional parameters for the header: --sample, --lib, --rg. See the manual for details.
  • PL:illumina is set by default in the SAM header

2012-04-06: mrFAST version 2.1.0.6 release:

• Support for read length up to 1000 bp.
• Edit distance now defaults to 4% of the read length, and can still be changed through the -e parameter.
• Bug that caused a slight reduction in sensitivity is fixed.
• The batch mode (-b) is deprecated. Input the reference as multi-sequence FASTA file only.

2012-03-07: mrFAST version 2.1.0.5 release:

• Automatic detection of FASTQ quality offset. mrFAST now rescales quality offset to 33 (Sanger format) if the input offset is 64.
• --maxdis parameter now defaults to 300, and --maxoea defaults to 100. To disable, pass --maxdis 0 and/or --maxoea 0.
• In paired end mode, best concordant and best discordant mapping files are merged into a single SAM file.
• Bug fixes in the CIGAR string generation in paired end mode.
• --discordant-vh option is now selected by default in paired end mode.

2012-02-21: mrFAST version 2.1.0.4 release:

• Better memory management in paired-end mode.
• Sample set is added (genome file, sequence files, command line and expected output).

2011-12-15: mrFAST version 2.1.0.3 release:

• Segmentation fault when main memory is unsufficient is fixed.

2011-12-03: mrFAST version 2.1.0.2 release:

• Bug in parsing parameters is fixed (bug #3436724).
• Unused memory allocations cleaned.

2011-11-07: mrFAST version 2.1.0.1 release:

• Segmentation fault when CIGAR string is too large is fixed (long sequences, with high edit distance).
• Several typos in error messages are fixed.
• Program crash when incorrect parameters are entered is fixed.
• If the length of the pairs of reads in paired-end mode are different, mrFAST now trims the longer end to match the shorter end sequence.
• Compilation warnings with some versions of gcc are cleaned.

2011-09-12: mrFAST version 2.1.0.0 release:

• Several bugs are fixed.
• New parameter --maxoea now limits the maximum number of locations for one end anchored (OEA) sequences. This will help substantially reduce the output file size. For NovelSeq use, we recommend to set this parameter to at least 100.
• New parameter --maxdis now limits the maximum number of locations for discordant read pairs in the DIVET file. This will help substantially reduce the output file size. For VariationHunter use, we recommend to set this parameter to at least 300.

2010-09-26: mrFAST version 2.0.0.5 release:

• Several minor bugs are fixed.
• Sequence and quality information of the unmapped ends of OEA pairs are added to the SAM-compatible OEA output file for NovelSeq. Next release of NovelSeq will be able to parse this file. Please contact NovelSeq authors if you need help with format conversion in the mean time.
• User manual uploaded.

2010-08-26: mrFAST version 2.0.0.3 release:

• One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq added. The output format is SAM, please contact NovelSeq authors if you need help with format conversion.

2010-07-24: mrFAST version 2.0.0.2 release:

• Minor bug in VariationHunter output (--discordant-vh) in reporting probability score is fixed.

2010-06-30: mrFAST version 2.0.0.1 release:

• Minor bug in VariationHunter output (--discordant-vh) is fixed.

2010-06-21: mrFAST version 2.0.0 release:

• New semi-cache-oblivious algorithm to improve mapping speed.
• Longer reads and more indels are supported.
• Improved user interface similar to mrsFAST.
• SAM format output.