A unified framework for multi way local ancestry deconvolution with high density SNP data
 Maintainer: Gaston K. Mazandu <kuzamunu at aims.ac.za>, Bioinformatics and Genomics Informatics Tools
 Contributors: Ephifania Geza1, 2, Nicola J. Mulder1, Emile R. Chimusa3 and Gaston K. Mazandu1,2,3

 

(1) Computational Biology (CBIO) Group, Department of integrative Biomedical Sciences, Institute of Infectious Disease and Molecular
    Medicine (IDM), University of Cape Town (UCT), Observatory 7925, South Africa

 

(2) African Institute for Mathematical Sciences (AIMS), Melrose Road, Muizenberg 7945, South Africa

 

(3) Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape
    Town (UCT), Observatory 7925, South Africa

 

The FRANC Interface

A framework that allows a user to estimate the ancestry of each chromosomal segment of an admixed individual, commonly known as local ancestry inference or local ancestry deconvolution.

FRANC includes eight commonly used existing state-of-the-art tools, namely WINPOP, LAMPLD, SUPPORTMIX, RFMIX, PCADMIX, ELAI, CHROMOPAINTER and LOTER. It enables users to run more than one tool on one or more chromosomes simultaneously and to choose output formats that may ease their use in further local ancestry deconvolution applications with a single line command.


Documentation

To view the documentation for the version of the FRANC interface downloaded in your system, go to the franc_interface directory and type the following command line:

python setup.py --long-description

Refer to the PDF version of the documentation below for more information on the FRANC interface administration and usage, as well as information on different multi-way ancestry deconvolution tools included in this interface.

 

TXT Show Library Source FRANC
PDF   Reference Manual

Details

Description Python framework for local ancestry inference integrating eight existing state-of-the-art ancestry deconvolution tools that uses high density SNPs data.
Version 19.1
Depends Python (≥ 2.7.x), Perl, R
License GPL (>= 3)
Requires zlib1g-dev, scikit-allel, libpng12.so.0
SystemRequirements OS Independent, but tested only on Linux (Ubuntu)
Release date Wednesday 09th January, 2019 −12:00

Package Archives

Follow FRANC administration and usage instructions in the PDF and txt documentation files to optimally use this python interface.

Interface Source franc.tar.gz
Browse other tools A-DaGO-Fun Package

Functions and tools included»

The main functions and tools in the FRANC Interface are:

  • franc and convertall python modules in the franc_interface folder.
  • FRANC integrates existing multi-way ancestry deconvolution tools in the franc_util/soft folder.

Important notes:

  • Currently, FRANC includes eight most commonly used tools, providing users with a wide range of choices.
  • It manipulates tool-specific inputs, deconvolves local ancestry and standardizes outputs, easing local ancestry estimate process.


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Mailing Lists»

An appropriate FRANC forum is still to be implemented, for now, any problem accounted when using this tool or comments should be forwarded by email to the FRANC team:

 Acknowledgements

Any work dependent on open-source software owes debt to those who developed these tools. The authors thank everyone involved with free software, from the core developers to those who contributed to the documentation. Many thanks to the authors of the freely available libraries for making this work possible. This work received no specific funding.

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