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.
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