These are a series of tutorials that were initially developed for teaching introductory bioinformatics classes at Virginia Tech. Over time they have grown to include smaller protocols used in the Aylward lab group.

The "chapters" or tutorials below are intended for use at the introductory level (i.e., starting with little or no bioinformatics knowledge). They presume access to a Unix environment and have been tested on Ubuntu or CentOS systems.

How to use these tutorials

The first ~10 or so tutorials are ordered logically, with each building on methods/tools introduced in previous sections. It is therefore best for those just starting in bioinformatics to start from the beginning and progress gradually. Some of the tutorials only have GitHub markdown sheets with instructions, and they can be followed in the command line with no prior setup required. Others have additional files that are needed to complete the tutorials; for these it is best to download the tutorial folder/directory and run the code there. As an example...

Introductory bioinformatics tutorials

Introduction to basic Unix commands
Introduction to the Unix environment - useful commands - navigating directories

Introduction to working with FASTA files
Introduction to DNA and protein sequences in FASTA format - parsing files with seqkit

Introduction to gene prediction with Prodigal
Downloading genomes from NCBI - Predicting protein-coding genes with Prodigal - predicting rRNA genes with barrnap

Introduction to homology searches with BLAST
Introduction to homology searches - BLAST databases - running BLASTP - parsing BLAST outputs

Ch. 2: Introduction to Whole Genome Annotation
Introduction to HMMs - alignments - differences with BLASTP

Ch. 2: Introduction to Multi-Sequence Alignments and Phylogenetics
- - - -

Giant virus genomics

Screening giant virus bins with Viralrecall
Introduction to homology searches - BLAST databases - running BLASTP - parsing BLAST outputs


Making a concatenated marker gene tree for giant viruses
Introduction to homology searches - BLAST databases - running BLASTP - parsing BLAST outputs

Phylogenomics and pan-genomics of bacteria and archaea

Making a phylogenetic tree based on a concatenated marker gene alignment
markerfinder - tree certainty


Calculating N-ARSC and C-ARSC from whole-genome predicted proteomes