medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
Show all available versions of medaka:
$ module avail medaka
Load one version into your environment and run it:
$ module load medaka/1.4.3 $ medaka -h
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/medaka/1.4.3 $ sudo chown -R aorth:aorth /export/apps/medaka/1.4.3 $ module load python/3.7 $ python3 -m venv /export/apps/medaka/1.4.3 $ source /export/apps/medaka/1.4.3/bin/activate $ pip install --upgrade pip setuptools $ pip install medaka==1.4.3 $ sudo chown -R root:root /export/apps/medaka/1.4.3