User Manual

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

NOTE: mrFAST is developed for Illumina, thus requires all reads to be at the same length. For paired-end reads, lengths of mates may be different from each other, but each "side" should have a uniform length.

If the lengths of the reads are not the same in a file, it may crash or output incorrectly formatted SAM files.

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Citations

Personalized copy number and segmental duplication maps using next-generation sequencing. Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler. Nature Genetics, Oct, 41(10):1061-1067, 2009.

Accelerating read mapping with FastHASH. H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu, C. Alkan. BMC Genomics, 14(Suppl 1):S13, 2013.

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General

Please pull the latest version from GitHub or download from Sourceforge page. Run 'make' to build mrFAST.

mrFAST:

1. generates an index of the reference genome and
2. maps the reads to reference genome.

Requirements:

• zlib for the ability to read compressed FASTQ and write compressed SAM files.
• C compiler (mrFAST is developed with gcc versions > 4.1.2)

Building

On Unix/Linux systems, we recommend using GNU gcc version > 4.1.2 as your compiler and type 'make' to build. Example:

``linux> make

gcc -c -O3 baseFAST.c -o baseFAST.o gcc -c -O3 CommandLineParser.c -o CommandLineParser.o gcc -c -O3 Common.c -o Common.o gcc -c -O3 HashTable.c -o HashTable.o gcc -c -O3 MrFAST.c -o MrFAST.o gcc -c -O3 Output.c -o Output.o gcc -c -O3 Reads.c -o Reads.o gcc -c -O3 RefGenome.c -o RefGenome.o gcc baseFAST.o CommandLineParser.o Common.o HashTable.o MrFAST.o Output.o Reads.o RefGenome.o
-o mrFAST -lz -lm rm -rf *.o''