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LINUX Version
replaced with gcc binary on May 24, 2011
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Download the following file,

maps_LINUX.tar.gz

Uncompress maps_LINUX.tar.gz
% gunzip maps.tar.gz

Untar maps.tar
% tar -xf maps.tar

Move into the maps directory.
% cd maps

There are three binary files of maps programs (mkindex, mpsmap, psmap) compiled under CentOS 5.3
Change mode to make them executable.

% chmod +x mkindex
% chmod +x mpsmap
% chmod +x psmap


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MAC OSX Snow Leopard Version
replaced with gcc binary on May 24, 2011
-------------------------------------------------

Download the following file,

maps_MACOSX.tar.gz

Open Terminal, and place the downloaded file to whereever you want, for instance, to your home directory.

% mv ~/Downloads/maps.tar.gz .
Sometimes, the system automatically uncompress the file, and you already have maps.tar or maps directory. then do
% mv ~/Downloads/maps.tar .
or
% mv ~/Downloads/maps .
instead,

Uncompress, if you have maps.tar.gz
% gunzip maps.tar.gz

Untar, if you have maps.tar
% tar -xf maps.tar

Move into the maps directory.
% cd maps

There are three binary files of maps programs (mkindex, mpsmap, psmap) compiled for MacOSX 10.6.5 (Snow Leopard).
Change mode to make them executable.

% chmod +x mkindex
% chmod +x mpsmap
% chmod +x psmap


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Quick start:
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There are sample files of PhiX reference (PhiX.fasta), and Illumina reads (reads.fastq) in the same directory.

Type following commands to create a postscript file.

% ./mkindex -10 PhiX.fasta
% ./mpsmap -i 10 -a 2 -r 3 -h 2 -job h2 PhiX.fasta reads.fastq
% ./psmap -bw 1 -cc -job h2 PhiX.fasta reads.fastq
% open reads.fastq_h2_bw.ps

mkindex creates the index file PhiX.fasta.10
mpsmap performs the mapping and creates a hit file reads.fastq_h2.hit and other files
psmap creates the mapping drawing as a postscript file
open opens the postscript file with Mac's Preview apprication
saving the drawing in pdf format from Preview saves file size.

Replace the file names to analyze your data.
Typing commands without argument will show some usage of options.


maps programs are distributed "as is", free of charge, and without warranty of any kind.
We appreciate it if you acknowledge use of maps in any reports or publications.

Contact: kensuke-nm @ is.naist.jp

K.Nakamura,T.Oshima,T.Morimoto,S.Ikeda,H.Yoshikawa,Y.Shiwa,S.Ishikawa,M.C.Linak,A.Hirai,H.Takahashi,Md.Altaf-Ul-Amin,N.Ogasawara and S.Kanaya, "Sequence-specific error profile of Illumina sequencers",Nucleic Acids Research, (2011) doi:10,1093/nar/gkr344.

Copyright 2010 Kensuke Nakamura NAIST, All rights reserved.