Computational Genomics

Explore computational genomics through a comprehensive 6-hour course from San Diego State University. Delve into genome sequencing technologies, DNA assembly techniques, and bioinformatics tools. Learn about AWS for genomic analysis, BLAST algorithms, antibiotic resistance mechanisms, and advanced k-mer counting methods. Gain practical skills in metagenome binning, genome consistency checking, and subsystem classification. Suitable for students and professionals seeking to enhance their understanding of modern genomic analysis techniques and their applications in microbiology and antibiotic resistance research.

About Dr. Rob Edwards.
Learning Outcomes.
Why we are going to use AWS in the course.
Create Amazon Web Services Student Account.
Start AWS Computational Genomics Image.
SSH Keys.
Central Dogma.
What does it mean to sequence a genome?.
What is genome sequencing part 1.
What is genome sequencing part 2.
Steps In Genome Sequencing.
Sanger sequencing.
454 pyrosequencing.
Introduction to Illumina Sequencing.
illumina paired end sequencing.
Ion Torrent Sequencing.
Pacific Biosciences Sequencing.
Oxford Nanopore ONT Sequencing.
Definitions.
An overview of DNA sequence assembly.
Naive DNA sequence assembly.
Greedy Assembly of DNA Sequences.
Overlap layout consensus sequence assembly approach.
de Bruijn graph assembly for DNA sequences.
Why does paired end sequencing help assembly?.
Assembly problems 1 ... repeats.
Assignment1.
Assignment 1 solution.
Assignment 3.
BLAST 1.
BLAST 2 seed and extend.
BLAST 3 amino acid differences.
BLAST 4 PAM vs BLOSUM.
BLAST 5 BLOSUM62.
BLAST 6 scoring alignments.
BLAST 7 scoring gaps.
BLAST 8 Probability.
BLAST 9 E values.
BLAST 10 Algorithms.
BLAST 11 PSWM.
ESKAPE Pathogens.
Klebsiella Introduction.
Antibiotics 1 mode of action.
Antibiotics 2 mechanisms of resistance.
Antibiotics 3 Role of HGT in antibiotic resistance.
Antibiotics 4 Resistance Timeline.
Antibiotics 5 resistance databases.
Subsystems Introduction.
Subsystem Classification.
Subsystems How to Annotate Genomes and Metagenomes.
Introduction to k-mers.
Introduction on counting k-mers.
k-mer algorithms: Compare and Swap.
Bloom Filters.
Counting k-mers with Bloom filters.
Count Min Sketch.
Counting Quotient Filters.
Metagenome Binning.
CheckM for Genome Consistency.
Genome Peek.
ABACBS Presentation 2020.