Cervicovaginal Microbiome and Virome During ART and HIV Discordant Shedding

This repository contains code for the manuscript Longitudinal cervicovaginal microbiome and virome alterations during ART and discordant shedding in women living with HIV, in review at Nature Communications. Link to preprint: https://www.researchsquare.com/article/rs-4078561/v1

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Contents:

1. Bacterial microbiome sequencing analysis:

• Bacterial_QC_classification.sh: Commands and instructions for QC of raw bacterial metagenomic sequencing data and classification of clean reads.
• parse_krakenuniqreports_mpa.py: Python script to parse combined KrakenUniq outputs to desired taxonomic level.
• Bacterial_diversity_taxonomic.R: R script for ecological and statistical analysis of bacterial taxonomic profiles.
• Bacterial_diversity_functional.R: R script for ecological and statistical analysis of bacterial functional profiles.

2. DNA virome sequencing analysis:

• DNA_virome_QC_contigs.sh: Commands and instructions for QC of DNA virome (MDA) metagenomic sequencing data; contig assembly; viral contig identification and classification; mapping clean reads back to viral contigs.
• DNA_virome_analysis.R: R script for ecological and statistical analysis of virome profiles.
• Anellovirus_phylogeny.sh: Commands and instructions for building the anellovirus phylogeny.
• Anellovirus_analysis.R: R script for downstream analyses of anellovirus diversity.
• Papillomavirus_phylogeny.sh: Commmands and instructions for building the papillomavirus phylogeny.
• Papillomavirus_analysis.R: R script for downstream analysis of papillomavirus diversity.

3. DNA/RNA virome sequencing analysis:

• DNA-RNA_Virome_QC_blastx.sh: Commands and instructions for QC of DNA/RNA virome (SIA) metagenomic sequencing data and classification of clean reads.