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.

• 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 extra fix for library linking.

See which versions of marginpolish are available:

$ module avail marginpolish

Load one into your environment and run it:

$ module load marginpolish/1.0.0
$ marginPolish

Notes from the sysadmin during installation:

$ 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