Table of Contents

Command Line Basics and Useful Programs

• Introduction to Unix
  • Unix Basics 1
  • Introduction to Job Scheduling: SLURM
  • Introduction to GNU parallel
  • Introduction to HPC
  • Unix Admin commands
  • Grep
  • Sed
  • Introduction to regular expression
• HPC
  • How to Install a Program
  • SSH
    • SSH Shortcuts
    • Password-less SSH
  • SLURM
    • SLURM Cheatsheet
    • Creating SLURM job submission scripts
    • Submitting dependency jobs using SLURM
  • XSEDE
    • XSEDE supercomputer
    • XSEDE supercell storage
  • Containers
    • Introduction to Containers
    • Creating Containers Using Singularity
    • Modifying Existing Containers
• Bioawk
  • Bioawk Basics
• Viewing Files In Remote Machine Without Downloading

Project Management

• Introduction to Project Management
• Project Management Tools
  • Introduction to Slack
  • Introduction to GitHub
  • Introduction to Markdown
  • Zenhub Download

Introduction to BLAST

• BLAST example: finding a gene in a genome
• Running BLAST in parallel

Experimental Design

• Biological system
• Sequencing Technology
• Costs
• Generic Examples of Experimental Design
• List of Biology exceptions and irregularities

Data Acquisition and Wrangling

• File Transfer
  • File Transfer using wget
  • File Transfer using Globus
  • File Transfer using irods
  • File Transfer using SRA toolkit
• Data Sets Used in the tutorials
• FASTA manipulation
  • Determining Sequence length
  • Converting FastQ to FASTA
  • FASTQ Quality trimming
  • Retrieving FASTA file using sequence ID
• Manipulating Excel data sheets
  • Create Workbook from Multiple Text Files
  • Export multiple worksheets as separate text files
  • Create Index for All Worksheets
  • Merge two spreadsheets using a common column
• Data Management
  • Deposition of Data to NCBI SRA

Bioinformatics Terminology

• Reads, Contigs, Scaffolds and Chromosome
• File Formats
• Fasta Quality Score

RNA Sequencing

• RNA-Seq Example with a Genome Assembly
• RNA-Seq Example without a Genome Assembly
• Different Expression Analysis:DESeq2
• 10x genomics single-cell RNAseq analysis from SRA data using Cell Ranger and Seurat
• Using RSeQC to identify strand information of RNAseq

Genome Assembly and Annotation

• Introduction to Genome Assembly
• Introduction to Canu
  • Canu on XSEDE Bridges Super Computer
• Introduction to SPAdes
• Introduction to MaSuRCA

Genome Assembly Examples

• Bacillus thuringiensis data set
  • Canu Assembly of Bacillus thuringiensis
  • SPAdes Assembly of Bacillus thuringiensis
• Arabidopsis thaliana data set
  • MaSuRCA assembly of Arabidopsis thanliana
  • Short read assembly using Platanus
  • Iteration of Pilon polishing and gap-filling on a genome
  • Iterating a long read assembly to get higher contiguity by eliminating contaminant reads

Tools for Assessing the Quality of a Genome Assembly

• GenomeScope to Estimate Genome Size
• Checking a genome for contamination from vectors using UniVec
• Check a genome for PhiX contamination

Tools for Scaffolding Assemblies

• Genome Scaffolding Using Synteny with Pyscaf
• Hi-C scaffolding

Genetic Map Construction

• Generating Genetic Maps from GBS data
• Using Genetic Map to create AGPs

Introduction to Genome Annotation

• Calling Genome Methylation with Nanopolish and Comparing Promoter Methylation among Samples
• Introduction to Maker Gene Prediction
• Introduction to Braker2 Gene Prediction
• Motif Identification and Finding with MEME and FIMO

Comparative Genomics

• Positive, Neutral, Negative Selection with Codeml using Multiple Genome Annotations
• Gene Orthology, Synteny, and Visualzation with Opscan, Iadhore and Circos
• Gene Orthology, Synteny, and Visualzation with Orthofinder, Iadhore and Circos
• Gene Overlap Significance Testing with R Gene_overlap Package
• Phylostratiophraphy:Determining the LCA of all Genes in a Genome

Variant Discovery

• FreeBayes variant calling workflow for DNA-Seq
• GATK Best Practices Workflow for DNA-Seq
• SNP calling for GBS data using Stacks pipeline
• SNP calling for GBS data using Tassel pipeline (GBS.v2)

Metagenomics

• Quality control, assembly and mapping
• Qiime2
• DADA2
• Kraken2

Genome Repeat Identification

• Helitron Identification in a Genome Sequence
• DNA Transposon Annotation with Inverted-Repeats Finder
• LTR Retrotransposon Annotation with LTR-Finder
• Repeat Annotation from Next-gen Sequencing Reads Using RepeatExplorer
• De-Novo Repeat Identification and Annotation from Genome Assemblies using RepeatModeler and RepeatMasker
• Tandem Duplication Annotation in a Genome Assembly Using Mummer and RedTandem
• How to assess structural variation in your genome, and identify jumping transposons

ATAC-Sequencing

• ATAC-seq

Data Visualization

• Viewing Files Remotely without Transferring
• Setting up an R and RStudio Environment
• Creating Boxplots in R
• Creating Heatmaps in R
• Visulaize Gaps in the Genome assemblies
• Visulaize Chromosome Bands using Ideogram