README.md

De novo metagenomic marker pipeline

Pipeline

1. Human Infant Microbiome Dataset ("Babybiome")

• Kudos to Molly K. Gibson for excellent datasharing (Gibson MK, Wang B, Ahmadi S, et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature microbiology. 2016;1:16024.)

2. /src/query.py

• Based on magicBLAST, a new RNAseq BLAST mapper

3. /src/coverager.py & /scripts/test_coverager.sh

• Generation of BAMs with magicBLAST mapping to long reads (direct streaming from SRA)
• Building a histogram of read coverage
• Thresholding for uniform deep and broad coverage of long reads with short reads (indicator contigs)
• Using chi-squared test to check for uniformity
• Generating probability of long read in short read set

4. Gen. Classifier

• Separation by physiological features
• Male-Female
• Delivery mode

5. Probability of gene co-occurrence?