ILRI Research Computing

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====== kma ======
KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on our users demands.

===== Information =====

  * Version: 1.4.0
  * Added: March, 2022
  * Updated: February, 2023
  * Link: https://bitbucket.org/genomicepidemiology/kma

===== Usage =====

See versions that are available:
<code>$ module avail kma</code>

Load one version into your environment and run it:
<code>$ module load kma/1.4.11
$ kma</code>


===== Installation ======
Notes from the sysadmin during installation.

<code>$ cd /tmp
$ git clone https://bitbucket.org/genomicepidemiology/kma.git
$ git checkout 1.4.11
$ make -j4
$ sudo mkdir -p /export/apps/kma/1.4.11/bin
$ sudo cp kma kma_index kma_shm kma_update /export/apps/kma/1.4.11/bin</code>