Bioinformatics Tutorials

AUTHOR: Dr Asad Prodhan https://asadprodhan.github.io/

Bioinformatics analysis using remote supercomputers

Coding learning resources

01. Getting started with bioinformatics coding

Download genomic data from public repository

01. Genome sequence metadata [manual]

02. Genome sequence metadata [command line]

03. Genome sequences [manual]

04. Genome sequences using datasets [command line]

05. Genome sequences using wget [command line]

06. RefSeq genome sequences using wget [command line]

Introduction to R

01. Why graduate students should learn R?

02. Setting up RStudio

03. An Introduction to R Coding

04. Data visualisation and analysis in R

Introduction to Bash

01. Command Line Basics

02. How to extract individual entries from a large fasta file

03. A Bash Script Showing Directory Properties in Linux

Introduction to bioinformatics coding

01. A beginner's guide to Bioinformatics

02. About the PATH

03. How to download genomes using the accession number

04. Downloading Genomes from RefSeq

Introduction to remote computing

01. How to connect to a remote Linux computer

02. How to connect to Pawsey’s Nimbus Instance

03. How to mount My Cloud NAS device to Linux computer

Nanopore sequencing data

01. An introduction to Nanopore DNA sequencing and data analysis

02. Reducing storage space by converting Nanopore fast5 files to slow5 using slow5tools

03. GPU-accelerated guppy basecalling

04. Automating sample labelling after Nanopore sequencing

05. How to channel sequencing reads from multiple subdirectories into nextflow pipeline

06. How to filter out contigs from a genome assembly file

07. How to extract individual entries from a large fasta file

08. Filtering out invalid characters from fastq reads

Some common bioinformatics analyses

01. Blastn (database download, execution, hit sequence extraction, and possible errors)

02. ANI (average nucleotide identity)

03. Bacterial ID (phylogenetic tree reconstruction using UBCG pipeline)

04. Kraken 2 (running on HPC using singularity container and nextflow?)

05. Miniasm (setting up and running miniasm assembler

06. phyloTree (an automated, reproducible, and scalable workflow for Bayesian phylogenetic analysis using Nextflow and Singularity)

07. phyloTreeHPC (an automated, reproducible, and scalable workflow for Bayesian phylogenetic analysis using a HPC cluster, Nextflow, and Singularity container)

08. How to extract individual entries from a large fasta file

Science writing

01. Publishing a paper. Professor Hans Lambers

Invited talks

01. An introduction to Nanopore DNA sequencing and data analysis. Nanopore Workshop for Biosecurity, Curtin University, Perth, Australia, 27-29 June 2023.

02. Preparing for a career after university. Career Development Workshop, UWA Society of Bangladeshi Culture (USBC), The University of Western Australia, Perth, Australia, 26 August 2023.

03. Command Line Basics. Nanopore Workshop for Biosecurity, Curtin University, Perth, Australia, 27-29 June 2023.

04. Introductory Bioinformatics: Where do I start? Murdoch Bioinformatics, Murdoch University, Perth, Australia, 04 April 2024.