Introduction

Typical workflow of NGS data analysis

---

05 16S Amplicon Analysis 🧫

In the 16S amplicon analysis chapter there is an introductory guide on conducting analysis using DADA2 followed by two interesting examples of "real-life" analysis pipeline with the data from studies on Crohn's and Parkinson's diseases.

---

04 Phylogenetics 🌳

In the Phylogenetics chapter there is a complete pipeline of simple research in phylogenetics, from working with NCBI (and other databases) to building trees, evaluating them, and getting some worthwhile results.

---

03 Whole Genome and Pangenome Analyses 🧬

In the Whole (pan)genome chapter there is a pipeline of whole genome and pangenome analyses with PanACoTA pipeline which includes genomes filtering with mash, annotating with prokka & prodigal, pangenome building with mmseqs, core genomes alignment with mafft and finally building phylogenetic tree with iq-tree.

---

02 Genomic Variation Analysis 🔬

In the Genomic Variation Analysis chapter there is a detailed guide how to conduct studies on Variant Calling using fastqc, trimmomatic, bwa, samtools, abra2, bcftools, snpEff & SnpSift.

---

01 Quality Control of Raw Data 💎

In the Quality Control chapter there is a detailed guide how to conduct quality control of raw data using fastqc and trimmomatic.