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marginpolish-software [2019/09/26 14:49] (current)
aorth created
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 +====== MarginPolish ======
 +MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.
  
 +===== Information =====
 +
 +  * Version: 1.0.0 (real version is 1.1.dev-a3c7def)
 +  * Added: September, 2019
 +  * Link: https://​github.com/​UCSC-nanopore-cgl/​MarginPolish
 +
 +Real version is ''​1.1.dev-a3c7def'',​ which is actually just ''​1.0.0''​ with an [[https://​github.com/​UCSC-nanopore-cgl/​MarginPolish/​issues/​6|extra fix for library linking]].
 +
 +===== Usage =====
 +
 +See which versions of marginpolish are available:
 +<​code>​$ module avail marginpolish</​code>​
 +
 +Load one into your environment and run it:
 +<​code>​$ module load marginpolish/​1.0.0
 +$ marginPolish</​code>​
 +
 +===== Installation ======
 +
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ cd /tmp
 +$ git clone https://​github.com/​UCSC-nanopore-cgl/​MarginPolish.git
 +$ cd MarginPolish
 +$ git checkout a3c7defe048c7ccc7247c620a81be059c007d0c4
 +$ git submodule update --init
 +$ mkdir build
 +$ cd build
 +$ scl enable devtoolset-7 bash
 +$ cmake3 ..
 +$ make
 +$ sudo mkdir -p /​export/​apps/​marginpolish/​1.0.0
 +$ sudo chown aorth /​export/​apps/​marginpolish/​1.0.0
 +$ sudo cp marginPolish /​export/​apps/​marginpolish/​1.0.0
 +$ sudo chown -R root:root /​export/​apps/​marginpolish/​1.0.0</​code>​
marginpolish-software.txt · Last modified: 2019/09/26 14:49 by aorth