A two-way classifier to characterize metagenomes based on short and long read technologies
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scripts
src
README.md

README.md

De novo metagenomic marker pipeline

Pipeline

  1. Human Infant Microbiome Dataset ("Babybiome")
  1. /src/query.py
  • Based on magicBLAST, a new RNAseq BLAST mapper
  1. /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
  1. Gen. Classifier
  • Separation by physiological features
  • Male-Female
  • Delivery mode
  1. Probability of gene co-occurrence?