Informatics-on-High-throughput-Sequencing-Data-Course-Summer-2020-

This is a summer training course at CCIC (Faculty of Computers and Information), Mansoura University, Egypt.

Course Description / aims

The contents of this workshop are prepared to introduce Bioinformatics as the intersection of informatics and Biology, and how Bioinformatics play an important rule in different areas of our life ranging from agricultural, environmental sciences to our healthcare system. Bioinformatics research has been accelerated with the advent of Next-Generation Sequencing, NGS, machines. These machines produce a deluge of genomic data that is required to clean, manage, process, analyze, and interpret to have a clear understanding of our biological system. We will help you in this course to gain different skills that are required to start your career as a Bioinformatician.

Target audience

Undergraduate and graduate-level students in biology, medicine, science, agriculture, pharmacy, veterinary medicine, biomedical engineering, bioinformatics and other related fields.

Learning Objectives

Participants will gain practical experience and skills to be able to:

1. Use basic Unix commands for managing genomic data.
2. Access and Manipulate different genomic databases.
3. Explore different file formats for biological data.
4. Perform quality control of sequencing reads.
5. Map and align sequencing reads.
6. Perform de novo assembly tasks.
7. Analyze small variant calling and their annotation.
8. Visualized NGS data using some visualization tools.

Pre-requisites

• Basic biology concepts
• Basic computer skills

Course Agenda and Materials

Day	Objective	Materials
1	Difference among Bioinformatics, Medical Informatics, and Biomedical Informatics Bioinformatics Career in Egypt. How to Survive in Bioinformatics Field Introduction to Sequencing technologies (Three Generations of Sequencing Machines) Setup our working environment (Linux Virtual Machine using VirtualBox)	Day 1 session Day 1 session Video part1 Day 1 session Video part2
2	Unix-based Systems Why Linux for Bioinformatics What is Shell Getting Started with Command Line Interface, i.e. Terminal Playing with Linux Directory Tree Structure	Day 2 session Day 2 session Video part1 Day 2 session Video part2
3	Ownership of Linux files Understanding Linux Permissions Playing with Files using Unix/Linux commands	Day 3 session Day 3 session Video part1 Day 3 session Video part2
4	Linux Commands for System Managment (i.e. Process, Disk and Memory, etc.) Linux Commands for Archiving and Compression FASTA/FASTQ Files Format Understand Quality Scores and Phred+33 Format	Day 4 session Day 4 session Video part1 Day 4 session Video part2
5	Introduction to GTF files Searching FASTA/FASTQ/GTF files using grep command Regex with grep command (i.e. Counting reads in FASTA/FASTQ files) Piping the output of Linux commands	Day 5 session Day 5 session Video part1 Day 5 session Video part2
6	Piping/Redirecting output cut, sort, uniq, comm, and diff Linux Commands for networking and communicating with a remote machine	Day 6 session Day 6 session Video part1 Day 6 session Video part2
7	Introduction to Shell Scripting Variables in Bash User Inputs in Bash Arithmetic in Bash	Day 7 session Day 7 session Video
8	Numeric and String Comparisons If stataments, Nested If statements, If Else, If Elif Else, Boolean Operations Case Statements	Day 8 session Day 8 session Video part1 Day 8 session Video part2
9	While, Until, For loops Ranges and Select Statments Functions in bash	Day 9 session Day 9 session Video
10	What is SRA? How it is organized ? Playing with SRA toolkit	Day 10 session Day 10 session Video
11	What is FASTQC? Box and Whisker Plot Playing with FASTQC Modules?	Day 11 session Day 11 session Video part1 Day 11 session Video part2
12	Continue with FASTQC Modules Run FastQC in non-interactively mode Playing with Trimmomatic	Day 12 session Day 12 session Video
13	Sequence Alignment Programs BWA Aligner SAM file format	Day 13 session Day 13 session Video
14	Flag field in SAM format CIGAR statement in SAM format MD statement in SAM format Introduction to SAMtools	Day 14 session Day 14 session Video
15	Install SAMtools SAM <-> BAM Conversion SAMtools view, flagstat, sort, and index commands extract alignments using SAMtools view command Introduction to BED format	Day 15 session Day 15 session Video
16	What is Variant Calling, Examples of Genomic Variations SAMtools mpileup format SAMtools mpileup command	Day 16 session Day 16 session Video part1 Day 16 session Video part2
17	Variant Calling Pipeline Genotype Vs. Phenotype Vs. Alleles Vs. Haplotypes Genotype Vs. Phenotype Vs. Alleles Frequencies Phased/unphased Genotypes	Day 17 session Day 17 session Video
18	VCF/BCF format Generate VCF/BCF files with SAMtools	Day 18 session Day 18 session Video part1 Day 18 session Video part2
19	Generate raw VCF/BCF files with SAMtools Install BCFtools BCFtools view, call and mpileup commands Visualizing Alignment Information with SAMtools tview command Recap of Variant Calling Pipeline	Day 19 session Day 19 session Video
20	Recap of Variant Calling Pipeline	Day 20 session Video part 1 Day 20 session Video part 2

References

• Genomic Data Science Specialization from Johns Hopkins University
• Data Files