Lepto-Metagenomics

This repository include scripts for profiling microbial communities of 12 rat tissue samples using 9 different metagenomics profiling software. Also include profiling of 3 simulated samples of mice gut microbiome obtained from CAMI Challenge

All the profiling results and their downstream characterization statistics (alpha/beta diversity, differential abundant taxa) were compared and contrast.

Software included:

• BLASTN
• DIAMOND (BLASTX/MEGAN)
• Centrifuge
• CLARK
• CLARK-s
• KRAKEN2 (4 different databases)
  • minikraken
  • standard
  • maxikraken
  • customized (standard + with rat genomes built in)
• Bracken
• Kaiju
• METAPHLAN3

---

1.pre-process

• Quality check sequenced reads
• Map reads to host genomes to filter out host contaminations
• adapter trimming

2.run_profilers

• include metagenomics pipeline for 9 different profilers
• from database building/downloading
• to summarise profiling results
• convert profiles to BIOM format

3.MAG

• script to run nextflow pipeline MAG
• assemble and bin metagenomics reads

4.benchmark_downstream_analysis

• read profiling results of all software listed in 2.run_profilers into R
• compare and contrast profiling results of all software listed
• conduct alpha & beta diversity characterization for each sample
• conduct differential abundant analysis for each sample