tnatlas 0.0.3

Find transposon integrations in reads and align them to genomes.

Overview

TnAtlas is a Python package for identifying and annotating transposon integration events into genomes.

Given a set of sequencing reads, transposon sequences, and genomes, the TnAtlas package can:

• Looks for reads which contain genomic DNA preceded by transposon DNA.
• Annotating the reads with corresponding features from the genome.
• Produces a summary for a set of reads in excel format.

For those who do not want to write Python code, the package also ships with 2 utilities, tnfind and tnmeta, which can be used to run analysis from the command line.

Installing

Dependencies

• Python >= 3.8
• blastn >= 2.12

Optionally

Some parts of the pipeline also require

• fastqc (for sequencing quality control reports)
• sickle (for trimming based on sequencing quality)

From source code

1. Get the code:

   git clone https://github.com/lgrozinger/transposonaligner

2. Install using pip:

   python3 -m pip install ./transposonaligner

From PyPI (using pip)

Coming soon to PyPI...

Usage

Contributing

Contributions of all kinds are welcomed, including:

• Code for new features and bug fixes
• Test code and examples
• Bug reports and suggestions for new features (e.g. opening a github issue)

If you plan to change the source code, please open an issue for discussing the proposed changes and fork the repository.

Citing

If you use this work as part of a publication, please cite as: ___________________

Acknowledgements