minia kmer limit

Question

[orange]

Hi everyone

When I use minia 2.0.3 with kmer=141, it fails. But with kmer=127, it works!

So does minia have kmer limit?

Answer 1

[edrezen]

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.