Microbial DNA as a Diagnostic Marker for Hepatocellular Carcinoma

Data Preprocessing

Host Depletion

Host deplete all samples with 47 Pangenomes from the Human Pangenome Project, T2T-CHM13v2.0, GRCh38.p14 and PhiX (Host Depletion Repo)

• Input: Raw fastq files with mixed microbial and human reads
• Output: Fastq files with just microbial reads

Microbial Classification

Run SHOGUN + Woltka pipeline using RS210 -Clean

• Input: Fastq files with just microbial reads
• Output: Biom/taxonomy table for all samples including blanks

Lab-associated Decontamination

Run SCRuB to remove any lab associated contamination: 1_SCRuB_Decontamination.ipynb

• Input: Biom/taxonomy table for all samples including blanks
• Output: Decontaminated biom/taxonomy table for all biological samples

Mismapping Taxa Reduction

Run micov to determine which taxa may be falsely mapped and remove those taxa: 2_MicovFilter.ipynb

• Input: Decontaminated biom/taxonomy table for all biological samples from SCRuB + SAM files from host depletion
• Output: Decontaminated + mismapped taxa reduction biom/taxonomy table for all biological samples

Data Analysis

Beta Diversity Analysis

Beta diversity analysis using Qiime2 and RPCA

• Input: Decontaminated + mismapped taxa reduction biom/taxonomy table for all biological samples
• Output: Beta diversity differences across disease groups

BIRDMAn

Performing differential abundance using BIRDMAn, Genome data across disease groups data using Birdman.

• Input: Decontaminated + mismapped taxa reduction biom/taxonomy table for all biological samples
• Output: Top microbial features according to Birdman