paulmenzel / nanopype

Snakemake pipelines for nanopore sequencing data archiving and processing

Nanopype

Documentation

Detailed documentation and tutorials are available at readthedocs.

Nanopype is a snakemake based pipeline providing convenient Oxford Nanopore Technology (ONT) data processing and storage solutions.

The pipeline is split in a processing part including basecalling and alignment and an analysis part covering further downstream applications. A summary of all included tools is given in the tools section.

To get started the installation chapter describes the available installation options depending on the operation system, available hardware and already existing environments.

Recurring steps of the nanopore data analysis are covered under workflow for both local and cluster usage.

The modules part covers an in depth description of all available tools and workflows together with their respective configuration options. This section is the main reference of the pipeline.

Finally for new users the tutorial might be helpful to learn the general concepts and usage of the pipeline. To complete the tutorial the test reads included in the package are sufficient and no separate wet-lab experiemnt is required.