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'''K-tuple Alignment with Rapid Matching Algorithm'''
'''K-tuple Alignment with Rapid Matching Algorithm'''
Karma uses an existing reference to align short reads, such as generated by Illumina sequencers.
Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.
The current version, 0.9.0, is optimized to rapidly map base space reads from Illumina sequencers.
The current version, 0.9.0, is optimized to rapidly map base space reads from Illumina sequencers.
Color space and LS454 sequence alignments are not working. These features will return in Karma 0.9.1.
Color space and LS454 sequence alignments are not currently supported. These features will return in Karma 0.9.1.
= Download Karma =
= Download Karma =
= Build Karma =
= Build Karma =
Karma is designed to be reasonably portable.
However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, there are likely other portability issues.
We support Karma only on Ubuntu 9.10 on 64-bit processors.
== Dependencies ==
== Dependencies ==
== Building ==
== Building ==
Assuming the karma tar file is named karma.tgz, do the following
tar xvzf karma.tgz
cd karma-0.9
make
mkdir ~/bin
cp karma/karma ~/bin
Alternatively, if you want to share the karma binary install it in /usr/local/bin/karma.
== Testing the build ==
== Testing the build ==
