Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
See versions which are available:
$ module avail nanopolish
Load one version into your environment and run it:
$ module load nanopolish/0.14.0 $ nanopolish help
Notes from the sysadmin during installation:
$ cd /tmp $ git clone --recursive https://github.com/jts/nanopolish.git $ cd nanopolish $ git checkout v0.14.0 # Load the htslib and minimap2 modules because they provide necessary # CPPFLAGS and LDFLAGS for the build $ module load htslib/1.15.1 minimap2/2.24 $ HTS=noinstall MINIMAP2=noinstall make $ sudo mkdir -p /export/apps/nanopolish/0.14.0 $ sudo chown aorth:aorth /export/apps/nanopolish/0.14.0 $ cp -r bin docs nanopolish test scripts README.md LICENSE /export/apps/nanopolish/0.14.0 $ module load python/3.8 $ python3.8 -m venv /export/apps/nanopolish/0.14.0/venv $ source /export/apps/nanopolish/0.14.0/venv/bin/activate $ pip install -r scripts/requirements.txt $ sudo chown -R root:root /export/apps/nanopolish/0.14.0