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?