{"id":21134215,"url":"https://github.com/cometsong/ma-genta","last_synced_at":"2025-03-14T12:41:42.443Z","repository":{"id":141630465,"uuid":"189293258","full_name":"cometsong/MA-GenTA","owner":"cometsong","description":"Targeted Probe Design Pipeline. 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We present a quantitative, straightforward, cost-effective method for microbiome profiling that combines desirable features of both approaches termed MA‑GenTA: Microbial Abundances from Genome Tagged Analysis. MA-GenTA employs highly multiplexed oligonucleotide probes designed from reference genomes in a pooled primer-extension reaction during library construction to derive relative abundance data. To test the utility of the MA-GenTA assay, probes were designed for 830 high quality metagenome-assembled genomes representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, NMDS clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS and 16S rRNA datasets.  MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes.\n\n----------\n## Overview:\nThere are 4 components of the MA-GenTA assay presented here. \n\n1. Probe design pipeline - this pipeline starts with reference genomes for probe design, filtering, and ends  with probe selection.\n\n2. Probes used in MA-GenTA - these are the probes used in the MA-GenTA assay.\n\n3. Data processing - starting with raw sequencing reads ending with count tables of MAGs and probes per sample.\n\n4. Downstream analysis - starting with count tables and ending with statistical analyses and figure generation. \n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fma-genta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcometsong%2Fma-genta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fma-genta/lists"}