Skip to content

How to use Nanocompore

Nanocompore was designed to be used either through a python API or a command line interface. The package contains 3 main modules: SampComp, SampCompDB and SimReads

SampComp

This is the main module which compares the signal of 2 experimental conditions. It takes Nanopolished datasets as input and generates a database containing all the results as output. SampComp has to be run first either through the API (nanocompore.SampComp.SampComp) or the CLI (nanocompore sampcomp).

SampCompDB

SampCompDB is a wrapper around the DBM object database generated by SampComp. This module performs secondary statistical analyses and provide simple high level functions to plot, explore and export the results. At the moment SampCompDB is only accessible through the interactive python API (nanocompore.SampCompDB.SampCompDB). We strongly recommend to use jupyter notebook.

SimReads

This module can be used to generate artificial datasets based on a model file obtained from IVT generated RNA sequenced by direct RNA sequencing (Datasets, from the Nanopore RNA consortium). In addition, one can also simulate the presence of modifications by allowing to deviate from the model for selected positions.