Introduction

Nanalogue = Nucleic Acid Analogue

A common pain point in the genomics community is that BAM files are information-dense which makes it difficult to gain insight from them. Nanalogue hopes to make it easy to extract and process this information, and forms a companion to other tools such as samtools and modkit. Although nanalogue’s primary focus is on DNA/RNA modifications on a single-molecule level, some of its functions are quite general and can be applied to almost any BAM file. Nanalogue is open-source and its code can be found on Github. The code of a companion package pynanalogue can be found here.

If you are a developer who needs BAM files with defined single-molecule modification patterns to help develop/test your tool, nanalogue can also help you create BAM files from scratch using artificial data created using parameters defined by you.

This documentation site is under active development.

Usage

This book is divided into two parts, based on two out of the following three ways to use nanalogue:

• as a command line interface i.e. a tool that can be run from the terminal. See here.
• as a python library i.e. if you write python code, you can use pynanalogue, a wrapper around a subset of nanalogue’s functions. See here.
• as a rust library i.e. if you write rust code, you can benefit from nanalogue’s functions. If you are a rust developer looking to use nanalogue as a rust library, please head over to docs.rs.

Installation

General installation methods such as cargo install and pip install should work. For the most up to date information, please consult the README files from the Github links above.