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Platanus
- Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.
- First, it constructs contigs using the algorithm based on de Bruijn graph.
- Second, the order of contigs is determined according to paired-end (mate-pair) data and constructs scaffolds.
- Finally, paired-end reads localized on gaps in scaffolds are assembled and gaps are closed.
Platanus/1.2.1
- Version: 1.2.1
Usage
- Show all versions of platanus
$ module avail platanus ---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ---------------------------------------------------------------------------------------------- platanus/1.2.1
- Load a specific version
$ module load platanus/1.2.1
- Show help
$ platanus --help platanus --help Platanus version: 1.2.1 Usage: platanus Command [options] Command: assemble, scaffold, gap_close
Installation
- platanus comes already compiled, so all you have to do is unzip & copy to export-apps
mkdir ~/src/platanus cd ~/src/platanus wget http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201/platanus chmod +x platanus sudo mkdir -p /export/apps/platanus/1.2.1/ sudo cp platanus /export/apps/platanus/1.2.1/
- Create module file & push to github repo
#%Module1.0 ##################################################################### ## ## Platanus Modulefile ## By James Oguya, j.oguya@cgiar.org ## November, 2014 ## set appname platanus set version 1.2.1 set prefix /export/apps/${appname}/${version} set exec_prefix ${prefix} set url "http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/" set msg "Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.\nPlatanus Official Site: $url\n" module-whatis $msg proc ModulesHelp { } { puts stderr "$msg" } conflict platanus prepend-path PATH ${exec_prefix} - Clone repo on all compute nodes using ansible
ansible-playbook compute.yml --limit=compute --tags=modules -K
platanus-software.txt · Last modified: 2014/11/14 15:45 by joguya
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