AlleleFinder

Overview

AlleleFinder is a Python-based suite of tools designed for the discovery, sequence typing, and profiling of stx alleles in Shiga toxin-producing Escherichia coli (STEC). It provides a comprehensive solution for researchers and professionals working in the field of bacterial genomics.

Features

AlleleFinder offers seven main functionalities, each represented by a separate script:

1. profile_reduce: Reduces full wgMLST profile from Enterobase using genes of interest.
2. allele_translate_reduce: Translates allele files from Enterobase in nucleotide format to amino acid, performs content and length checks, and removes duplicates.
3. allele_find: Performs BLAST analyses on a nucleotide allele database against nucleotide query sequences to discover their sequence types.
4. allele_translate_find: Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.
5. aa_allele_find: Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.
6. allele_split: Splits a single allele database file into multiple files; one sequence per file.
7. allele_concatenate: Concatenates alleles of the stx A and B subunits into a single sequence with a linker.
8. stec_combined_subunits: Processes STEC alleles with both A and B subunits, performing subunit-level BLAST analyses and reporting.

Documentation

Detailed documentation for each script and general usage of AlleleFinder is available at the AlleleFinder GitHub pages site.

Quick Start

Conda is required to install AlleleFinder. See the documentation or AlleleFinder installation for instructions on getting conda installed on your system.

Create a new conda environment:

conda create -n allele_finder -c olcbioinformatics allelefinder

Additional installation instructions are available here.

Usage

Each script has specific input requirements and usage instructions. Please refer to the respective documentation for each script for detailed information:

• profile_reduce
• allele_translate_reduce
• allele_find
• allele_translate_find
• aa_allele_find
• allele_split
• allele_concatenate
• stec_combined_subunits

Feedback

We welcome your feedback. If you encounter any issues installing or running AlleleFinder, have feature requests, or need assistance, please open an issue on GitHub.

License

AlleleFinder is licensed under the MIT License. See the LICENSE file for more details.