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Introduction

Welcome to the handbook on NGS data analysis!
Once this was the library of manuals I used in work. Then I decided to deploy a website to make it more convenient for me to use. The best part of it that now anyone can use it too! Please enjoy!


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.