Metagenomic and metatranscriptomic insight into the roles of millipede hindgut microbiome

========

Analysis of 16S, metagenomes and metatranscriptomes included in the paper: Functional similarity despite taxonomical divergence in the millipede gut microbiota points to a common trophic strategy

Overview

├── 1_Bacterial_Colony_Counts_and_qPCR_Qunatification.Rmd

      ├── Control_qQPCR_ColonyC.ods
      
      
      ├── Control_qPCR_ColonyC.html
      
      
      ├── Control_qPCR_ColonyC.md

├── 2a_cutadapt_v2.0.sh

      ├── 2a_cutadapt.log

├── 2b_DADA2_16S_merge_V8.6.sh

      ├── 2b_run_DADA2_16S_V8.6.R

├── 2c_Decontamination.Rmd

      ├── 2c_Decontamination.md
      
      
      ├── 2c_Decontamination.html

├── 3_Community_ORFs_Classification_and Functional_Genes_Analysis.Rmd

      ├── 3_Community_ORFs_Classification_and Functional_Genes_Analysis.md
      
      
      ├── 3_Community_ORFs_Classification_and Functional_Genes_Analysis.html # Run after assembly (4a_Assembly.sh)

├── 4a_Assembly.sh

      ├── final.contigs.fa
      
      
      ├── options.json
      
      
      ├── log

├── 4b_MG_Mapping.sh

      ├── contigs.fa
      
      
      ├── name_conversions.txt
      
      
      ├── Sample.bam.bai
      
      
      ├── Sample.bam

├── 4c_MG_Anvio_database.sh

      ├── contigs.db
      
      
      ├── contigs-stats.csv
      
      
      ├── gene_calls.fa

├── 4d_MG_Centrifuge.sh

      ├── centrifuge_hits.tsv
      
      
      ├── centrifuge_report.tsv

├── 4e_MG_Profiling.sh

      ├── AUXILIARY-DATA.db
      
      
      ├── PROFILE.db
      
      
      ├── RUNLOG.txt

├── 5_Phylogenomics.sh

      ├── Metabat2_taxa_info-gtdb-tk.txt
      
      
      ├── Metabat2-phylogenomic-tree.txt

├── 6_MAG_Novelty_abundance.Rmd

      ├── 6_MAG_Novelty_abundance.md
      
      
      ├── 6_MAG_Novelty_abundance.html

├── 8_Abundance_of_Genes_MG_MT.Rmd

      ├── 8_Abundance_of_Genes_MG_MT.md
      
      
      ├── 8_Abundance_of_Genes_MG_MT.html

├── 9_CAZymes_Genes.Rmd

      ├── 9_CAZymes_Genes.md
      
      
      ├── 9_CAZymes_Genes.html

├── 10_Eukaryotic_abundance.Rmd

      ├── 10_Eukaryotic_abundance.md
      
      
      ├── 10_Eukaryotic_abundance.html

├── README.md # Overview of the repo

└── references.bib  # Bibtex formatted references cited in the RMD file

Viewing and reproducing the analysis

The MD files can be used to display the output on github, while HTML files can be used for offline viewing. The RMD files are best compiled using knitr on RStudio.