====== 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>