diff --git a/README.md b/README.md index 673b1ac..dae243f 100644 --- a/README.md +++ b/README.md @@ -27,24 +27,4 @@ _Typical workflow of NGS data analysis_ ┃ ┗ 📃05_03_Parkinsons_disease
┗ ℹī¸ README.md -_Handbook's structure_ - -## 05 16S Amplicon Analysis đŸ§Ģ - -In the [16S amplicon analysis folder](05_16S_amplicon_analysis) 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 đŸŒŗ - -In the [Phylogenetics folder](04_Phylogenetics) 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 đŸ§Ŧ - -In the [Whole (pan)genome analyses](03_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`. - -## 02 Genomic Variation Analysis đŸ”Ŧ - -In the [Genomic Variation Analysis folder](02_Genomic_Variation_Analysis) 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 folder](01_Quality_Control) there is a detailed guide how to conduct quality control of raw data using `fastqc` and `trimmomatic`. +_Handbook's structure_ \ No newline at end of file