📚 A repository of repositories containing bioinformatics tutorials and workflows.
View as a web page or Github repository.
🏃♂ R boot camp
A look at the basics of the R programming language to get you up and running on R. This bootcamp covers the following the installation of R & R Studio, the basics of R and how to read in data and inspect its contents.
A guide to the basics of R markdown and how to upload a project onto Github from R studio.
Visualisation of BLAST genome alignments with circos plots in R.
ANI and SNP distances together provide information about the relatedness of isolates. This workflow takes n genomes and compares them against each other to determine ANI % and SNP numbers, visualising both as heatmaps in python.
Geospatial mapping of ANI connections between bacterial strains at different geographical locations in Indonesia.
This workflow uses the Phyloseq package in R to cluster 16S rRNA data from the human microbiome project (HMP) and determine if it corresponds to a body site, such as saliva, stool, or sebum. The HMPv35 dataset is used which was sequenced from amplicons of the rRNA 16S variable regions 3-5.
This workflow uses miaverse packages in R to analyse short-read (Illumina) taxonomic-based metagenomic data from noma and healthy human saliva samples.
A guide to co-occurrence analysis of AMR genes which highlights the genetic location of AMR genes relative to each other across genomes with short-read genomic data.
An automated short-read bacterial genome assembly and analysis tool implemented in Snakemake. It takes paired-end gzipped fastq short-read files. It assembles and analyses the genomes producing a html report with MLST sequence typing and acquired AMR genes for multiple genomes.