MicroHapDB

NBFAC, 2018-2023 https://github.com/bioforensics/microhapdb

MicroHapDB is a comprehensive catalog of human microhaplotype variation. The database integrates marker and population frequency data from numerous published research articles. Allele frequency estimates and allelic diversity statistics ($A_e$) are computed for 26 global populations so that markers can be ranked and evaluated for various applications.

MicroHapDB is designed to be user-friendly for researchers, technology developers, and forensic practitioners, supporting a range of access methods from browsing and simple text queries to complex queries and full programmatic access via a Python API. It is designed as a community resource requiring minimal infrastructure to use and maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB.

Installation

See this page for complete installation instructions. If this isn't your first rodeo, the commands below are provided as a quick reference.

conda install -c bioconda microhapdb pytest
pytest --pyargs microhapdb --doctest-modules

Usage

MicroHapDB provides several methods to access the contents of a locally installed database. The MicroHapDB documentation includes a "Getting started" guide as well as a comprehensive reference for running MicroHapDB on the command line.

A particularly intrepid and curious user may also be so bold as to download the core database tables directly from GitHub.

MicroHapDB includes statistics for ranking markers, tools for panel design, and instructions for adding markers to a private local copy of the database.

Citation

If you use this database, please cite our work.

Standage DS, Mitchell RN (2020) MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data. Frontiers in Genetics 11:781, doi:10.3389/fgene.2020.00781.

MicroHapDB was created and is maintained by the Bioinformatics Group at the National Bioforensic Anaylsis Center (NBFAC).

Additional references are available on this page.