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Question: minia kmer limit
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gravatar for orange
4.5 years ago by
orange • 30
Korea, Republic Of
orange • 30 wrote:

hi,everyone

    when I use minia 2.0.3 with kmer=141,it fail.But with kmer=127,it work!

So minia have kmer limit ?
minia assembly • 1.4k views
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modified 4.5 years ago by edrezen • 720 • written 4.5 years ago by orange • 30
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gravatar for edrezen
4.5 years ago by
edrezen • 720
France
edrezen • 720 wrote:

Hello,

By default, this version 2.0.3 of minia supports kmer sizes up to 127.

If you want to use greater kmer size, you need to compile it with a maximum value of your choice; you can do the following (the k4 value should be a multiple of 32)

wget "http://gatb-tools.gforge.inria.fr/versions/src/minia-2.0.3-Source.tar.gz"
tar xvf minia-2.0.3-Source.tar.gz
cd  minia-2.0.3-Source
mkdir build
cd build
cmake -DSKIP_DOC=1 -Dk4=160 ..
make

Then you should have a minia command that will support kmer sizes up to 159.
ADD COMMENT • link modified 4 months ago by RamRS ♦ 26k • written 4.5 years ago by edrezen • 720
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