Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference
Local ancestry inference (LAI) reveals population compositions of an individuals chromo-somes, which empowers population genetics and genetic association studies of diverse populations. The recent availability of large genomic datasets from biobanks offers unprecedented opportunities for LAI. However, such datasets are typically only accessible from cloud-based platforms, and the lack of…
Local ancestry inference (LAI) is a technique that uncovers the genetic makeup of an individual's chromosomes, enabling researchers to study population genetics and the genetic associations of diverse populations. With the advent of large genomic datasets from biobanks, LAI has become more accessible than ever before. However, the high cost and complexity of existing LAI tools have limited their use for researchers with limited resources.
To address this issue, a new cloud-ready pipeline called Recomb-Mix Cloud has been developed. This pipeline is based on Recomb-Mix, a recently introduced efficient LAI method that focuses on individual variants while using fewer computational resources compared to other LAI methods that rely on genomic windows. Recomb-Mix Cloud offers a comprehensive pipeline, starting from selecting panel samples, aligning markers, constructing compact reference panels, running Recomb-Mix, and generating LAI calls in standard data formats.
In addition to the pipeline, Recomb-Mix Cloud provides a collection of pre-computed compact population reference panels. These panels, constructed using data from the Human Genome Diversity Project and the 1000 Genomes Project, facilitate faster and more accurate LAI calls. The results of Recomb-Mix Cloud's performance show that it is significantly cheaper and faster than FLARE and RFMix, two popular LAI methods.
Specifically, using Recomb-Mix Cloud with a pre-computed reference panel for whole-genome LAI analysis on the All of Us Researcher Workbench costs only $0.01 per sample, compared to $0.43 for FLARE and $4.58 for RFMix.
These impressive results position Recomb-Mix Cloud as an ideal solution for democratizing local ancestry-based genetics research using modern biobank-sized data. By reducing the computational burden and cost, Recomb-Mix Cloud makes LAI more accessible to resource-constrained researchers, ultimately expanding the scope of genetic studies and promoting a more inclusive understanding of human genetic diversity.
The Recomb-Mix Cloud pipeline and the compact reference panels are now available for use at https://github.com/ucfcbb/Recomb-Mix.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
