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 which versions are available:
$ module avail medaka
Load one version into your environment and run it:
$ module load medaka/1.12.1 $ medaka -h
Notes from the sysadmin during installation:
$ module load python/3.10 $ sudo mkdir -p /export/apps/medaka/1.12.1/.venv $ sudo chown aorth /export/apps/medaka/1.12.1/.venv $ python -m venv /export/apps/medaka/1.12.1/.venv $ source /export/apps/medaka/1.12.1/.venv/bin/activate $ python -m pip install -U pip setuptools wheel $ python -m pip install medaka==1.12.1 $ sudo chown -R root:root /export/apps/medaka/1.12.1