Tutorials

This website provides some stand alone tutorials for genomics, population, comparative steps.

Genomics

• Short Read Assembly - Using short-read Illumina data for assemby
• Long Read Assembly - Using long read Nanopore,PacBio
• Assembly Assessment - BUSCO, QUAST

• Annotation - Bacteria and Eukaryotic genome annotation (with emphasis on Fungi)

• Repeats and Transposons - Identify Transposons and Repetitive elements

• Pan-Genome Construction - Assembly of pan-genome with emphasis on Eukaryotic example

• Shotgun Metagenome - Assembly shotgun metagenomes

Comparative analyses

• Protein Homology Searches
• Automated Orthology with OrthoFinder
• Whole Genome Alignment
• Codon-based Gene analyses

Transcriptome

• Transcriptome Assembly
• RNA-Seq alignments to Genome
• RNA-Seq from pseudoalignment - With Kallisto, Salmon
• Quantifying and comparing RNA-Seq in R

Population Genomics

• Variant calling with GATK
• Variant calling with htslib tools
• Variant calling with freebayes
• Copy Number Variation
• Non-reference genomic analyses

Visualization

• JBrowse2 Genome Browser Basics
• Phylogenetic Tree Visualization

R-tools

• Tidyverse - data import, filter, manipulation
• Drawing Heatmaps in R
• Drawing data distributions with Boxplots, Histograms

Myco/Microbiome

• Metabarcode analyses with amptk
• Metabarcode analyses with QIIME1
• Metabarcode analyses with QIIME2

Taxonomy

• Query NCBI Taxonomy Database - Query NCBI Taxonomy database