microhapdb 0.12

Portable database of microhaplotype marker and allele frequency data

MicroHapDB

NBFAC, 2018-2025 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 managed as a community resource requiring minimal infrastructure to maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB. The primary interface to MicroHapDB is through the console command line, which provides methods for browsing, searching, and filtering the database contents. Full programmatic access is available via a Python API. Alternatively, users can access the database tables directly using a spreadsheet program such as Microsoft Excel.

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.

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.