Latinbiota - gut microbiome diversity in Latin America

Central repository with scripts and workflows for the analysis of the gut microbiome of the Latinbiota cohort

Main analysis workflows

VirSearch - Searching viral sequences in metagenomes

GubaScreen - Protocol for detecting Gubaphage genomes among a set of predicted viral sequences

MAGscreen - Workflow for the identification and curation of new microbial species

metaMAP - Mapping sequencing reads to reference genomes for detecting microbial species

AMR-profiler - Characterizing AMR genes in metagenomes

ml-microbiome - Machine learning pipeline for classification of microbiome data

Protean - Functional annotation of protein sequences

Directory scripts/data_processing contains R scripts used to parse and process data for analysis
Directory scripts/plotting R scripts used to generate figures for manuscript