User Guide

Welcome to the iTP-Seq user guide. This documentation will help you understand the iTP-Seq method and learn how to analyze iTP-Seq data using the itpseq library.

Getting started

iTP-Seq (inverse toeprinting coupled to next-generation sequencing) is a powerful method for characterizing bacterial translation landscapes. This guide covers the method and data analysis workflow.

• What is iTP-Seq? - Overview of the iTP-Seq method, applications, and comparison to other techniques

• Installation - Step-by-step instructions for installing the itpseq software package

• Pre-processing data to use with itpseq - Guidelines for organizing, formatting, and preparing data for analysis

• Command line analysis - Documentation for the itpseq command line interface

• Loading iTP-Seq data in Python - Instructions for loading and manipulating iTP-Seq data in Python

• Tutorials - Practical examples and walkthroughs for common analysis tasks

Analysis approaches

The itpseq package can be used in two ways:

1. Command line interface - Suitable for standardized analyses and batch processing. See the Command line analysis section for details.

2. Python module - For custom analysis pipelines and interactive exploration. Refer to the Loading iTP-Seq data in Python section for getting started and API reference for the Python API documentation.

Need help?

For new users, we recommend beginning with What is iTP-Seq? to understand the method, followed by the Installation guide to set up the software. The Tutorials section demonstrates typical workflows.

For bug reports or feature requests, please use the GitHub issue tracker: t-renault/itpseq#issues