NGS Data Analysis Manuals

The materials in this repository are based on educational courses I have taken
It can be used as a helpful repository with cheat-sheets for NGS studies.

Typical workflow of NGS data analysis

To recreate any of the steps of this manual please install:

conda env create -f ngs-manual.yml

And of cource do not forget to activate the envinronment!

conda activate ngs-manual

Much more to be disclosured soon:

• Reference-free approach in the comparative analysis of metagenomic data
• Whole Genome and Pangenome Analyses
• 16S Amplicon Analysis

Genomic Variation Analysis

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

Quality Control of raw data

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