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microdiversity

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Qasim-Hussain-Code / comparative_gut_brain_axis_metagenomics

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A genome-resolved metagenomics pipeline replicating the Sharon et al. (2019) gut-brain axis study. Features MEGAHIT de novo co-assembly, Bowtie2 competitive read recruitment, and Anvi'o single-nucleotide variant (SNV) microdiversity profiling.

metagenomics microbiome bowtie2 autism-spectrum-disorder microbial-ecology anvio megahit gut-brain-axis microdiversity single-nucleotide-variants read-recruitment gnotobiotic cecal-metagenome co-assembly genome-resolved-metagenomics prokaryote-genomics
  • Updated Jul 11, 2026
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Qasim-Hussain-Code / anvio_read_recruitment_analysis

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This pipeline implements competitive fragment recruitment to map metagenomic sequence space against a representative reference genome. In microbial ecology, read recruitment provides a quantitative window into the evolutionary dynamics of natural populations by measuring nucleotide-level polymorphism and consensus sequence divergence.

metagenomics population-genetics microbial-ecology anvio microdiversity single-nucleotide-variants strain-resolved-profiling omputational-biology
  • Updated Jul 2, 2026
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