De novo metagenomic marker pipeline Pipeline 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.) /src/query.py Based on magicBLAST, a new RNAseq BLAST mapper /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 Gen. Classifier Separation by physiological features Male-Female Delivery mode Probability of gene co-occurrence?