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Sample.zip 2011-06-19 24.0 MB
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Qamar 1.0.0.zip 2011-06-19 343.5 kB
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README 2011-06-19 1.3 kB
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Qamar 1.0.0

Qamar is a sophisticated tool for correcting sequencing errors; 
it is based on de Bruijn sequences and solves erroneous reads 
as the 1-mismatch string problem. The first release of this tool 
can correct sequences from Illumina/Solexa and Sanger 
high-throughput sequencing technologies. It is highly accurate, 
fast and works well for all kinds of reads, whether short or 
long or even mixed and whatever the genome sizes and coverage 
levels are.


INSTALLATION
------------

Qt libraries must be installed.
It can be downloaded from (http://qt.nokia.com/downloads)

To compile Qamar, simply run:

make


RUNNING QAMAR
-------------

 ./Qamar input ouput Type [kmer] [minFreq] [Iter]

such that:
 Type    = fasta or fastq.. the type of the input file
 kmer    = 8,9,10.......... (21 by default) the kmer length must be < 33
 minFreq = 1,2,3........... ( 2 by default) the frequency of kmers that should be corrected
 Iter    = 1,2,3........... ( 1 by default) Number of iterations


ACKNOWLEDGMENTS
---------------
Mohammed Sahli, Tetsuo Shibuya

This work was partially supported by the Grant-in-Aid from the Ministry 
of Education, Culture, Sports, Science and Technology of Japan.


CONTACT
-------
Mohammed Sahli: mohammed@hgc.jp
Tetsuo Shibuya: tshibuya@hgc.jp
Source: README, updated 2011-06-19