Helpful repository with cheat-sheets for NGS studies!
Typical workflow of NGS data analysis
📚NGS-Handbook
┣ 📕01_Quality_Control
┣ 📗02_Genomic_Variation_Analysis
┣ 📘03_Whole_(Pan)genome_Analyses
┣ 📙04_Phylogenetics
┃ ┣ 📃04_01_Intro_trees
┃ ┣ 📃04_02_Mining_Data
┃ ┣ 📃04_03_MSA
┃ ┣ 📃04_04_Trees
┃ ┣ 📃04_05_Root_Date
┃ ┣ 📃04_06_Phylogenomics
┃ ┣ 📃04_07_Visualization_Pro
┃ ┗ 📃04_08_Tanglegram
┗ 📓05_16S_Amplicon_Analysis
┃ ┣ 📃05_01_Introduction
┃ ┣ 📃05_02_Crohns_disease
┃ ┗ 📃05_03_Parkinsons_disease
┗ ℹ️ README.md
Handbook's structure
In the 16S amplicon analysis folder 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.
In the Phylogenetics folder 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.
In the Whole (pan)genome analyses 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.
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.
In the Quality Control folder there is a detailed guide how to conduct quality control of raw data using fastqc and trimmomatic.