About this guidebook
I INTRODUCTION
1 Introduction to holo-omics
2 Study design considerations
II FIELD PROCEDURES
3 About fieldwork
4 Sample collection
5 Sample preservation
III LABORATORY PROCEDURES
6 About labwork
- General considerations
- Procedures for generating multi-omic data
7 DNA/RNA extraction
8 Protein/metabolite extraction
9 Sequencing library preparation
IV BIOINFORMATIC PROCEDURES
10 About bioinformatics
- 10.1 Prepare your shell environment
- 10.2 Using snakemake for workflow management
11 Sequencing data preprocessing
- Preprocess the reads using fastp
- Splitting host and non-host data
12 Host genomics (HG) data processing
- 12.1 Host reference genome
- 12.2 Host genome resequencing
13 Microbial metagenomics (MG) data processing
14 Host transcriptomics (HT) data processing
- 14.1 Reference-based host transcriptomics (HT) data processing
- 14.2 Reference-free host transcriptomics (HT) data processing
15 Microbial metatranscriptomics (HT) data processing
- 15.1 Reference-based microbial metatranscriptomics (MT) data processing
- 15.2 Reference-free microbial metatranscriptomics (MT) data processing
16 Host proteomics (HP) data processing
17 Microbial metaproteomics (MP) data processing
V STATISTICAL PROCEDURES
18 About statistics
19 Single omic analyses
20 Data transformations
- 20.1 Transformations to account for statistical assumptions
21 Unsupervised exploration
- 21.1 Cluster analysis
  - 21.1.1 Hierarchical clustering
  - 21.1.2 Disjoint clustering
- 21.2 Dimension reduction and ordination
22 Supervised analysis
- 22.1 Regression methods
- 22.2 Classification methods
  - 22.2.1 Random Forests (RF)
  - 22.2.2 Support Vector Machines (SVM)
23 Multi-omic integration
24 Multi-staged omics integration
25 Meta-dimensional omics integration
VI RESOURCES
26 Useful links
- Data access
- Documentation
27 References

A Practical Guide to Holo-Omics

14.2 Reference-free host transcriptomics (HT) data processing

Contents will be added shortly.