This is the repository for Raman-Sorting Single-Cell Analysis of Minimetagenomics and Comparative Genomics
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
- trim and QC by
-
Mapping
- mapping trimmed reads to filtered contigs by
bowtie2
- processing mapping results by
samtools
- duplicates removal by
picard
- mapping trimmed reads to filtered contigs by
-
Binning
- contigs binning by
anvio
andCONCOCT
- QC for bins by manual refinement and
checkM
- contigs binning by
-
Functional Analysis
- metagenome-assembled genome (MAG) recognized by
gtdb-tk
- Gene Calling: ORFs identified by
metagenemark
andprodigal
- Gene Annotation: coding DNA sequences (CDSs) annotated by
kofamscan
- Metabolic Pathway: KEGG
- metagenome-assembled genome (MAG) recognized by
-
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
- MAG 16S rRNA extracted by
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
-
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
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