ComparativeMetaGenome

This is the repository for Raman-Sorting Single-Cell Analysis of Minimetagenomics and Comparative Genomics

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🦠 💦 Minimetagenomics Ananlysis

Code is stored in ./minimetagenomics/ with scripts and Snakemake-enabled workflow to achieve

• Assembly

  • trim and QC by trimmomatic
  • contigs assembly by SPAdes
  • statistics of assembled contigs by quast
  • filtration by anvio

• Mapping

  • mapping trimmed reads to filtered contigs by bowtie2
  • processing mapping results by samtools
  • duplicates removal by picard

• Binning

  • contigs binning by anvio and CONCOCT
  • QC for bins by manual refinement and checkM

• Functional Analysis

  • metagenome-assembled genome (MAG) recognized by gtdb-tk
  • Gene Calling: ORFs identified by metagenemark and prodigal
  • Gene Annotation: coding DNA sequences (CDSs) annotated by kofamscan
  • Metabolic Pathway: KEGG

• Taxonomy for MAG and others

  • MAG 16S rRNA extracted by PROKKA
  • MAG taxonomy identified by BLAST
  • Other contigs taxnomy analyzed by Diamond
  • Phylogenetic tree established by NCBI taxonomy tree

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🧬 🔬 Comparative Genomic Analysis

Code is stored in ./compgenome/ with workflow in JupyterNoteBook for comparative analysis,

with file names labeled by figure number to achieve data mining, analysis, and visualization.

Figure 1 for pipeline and Figure 4 for PAO metabolic models are designed by Microsoft Powerpoint.

• Genome-scale metabolic modeling (GEMs) establishement and curation

  • Establish from .faa file using CarveMe
  • Improve and check quality of the GEM models using MEMOTE
  • Optimize and incorporate the ppk and ppx reactions into the GEMs if the genes are detected within the genome using COBRApy

• Microbial metabolic & ecological interaction analysis

  • Microbial metabolic interaction based on GEMs using SMETANA

• Comparative phylogenetic analysis

  • Stochastic OU process was applied to guide evolutionary pathways to improve the phylogram tree
  • Blomberg K statistic was calculated based on the R code with demonstrations in R Markdown

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🧰 💻 Operon Analysis

Online web server was applied based on Operon Mapper published in Bioinformatics.

This is applied with the aim to identify operon for ppk and ppx