1. Course material

1.1. List of Tools

Data quality control and preprocessing

• fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

• AdapterRemoval: https://github.com/MikkelSchubert/adapterremoval

Taxonomic classification of shotgun sequencing data

• kraken: https://ccb.jhu.edu/software/kraken/

• kraken2: https://ccb.jhu.edu/software/kraken2/index.shtml

• braken: https://ccb.jhu.edu/software/bracken/

• metaphlan3: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0

Visualization of taxonomic classification

• krona: https://github.com/marbl/Krona/wiki

• pavian: https://ccb.jhu.edu/software/pavian/

R packages for data analysis

• phyloseq: https://joey711.github.io/phyloseq/

• vegan: https://rdrr.io/cran/vegan/man/vegan-package.html

• ggplot2: https://ggplot2.tidyverse.org

• microbiome: https://microbiome.github.io/tutorials/

• DESeq2: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Other tools:

• taxaranks: https://github.com/linzhi2013/taxonomy_ranks/blob/master/README.md

1.2. Datasets to download

In the links below download the material needed for this course:

• Linux cheatsheet - summary of the most used commands in Linux.

• Fastq files 1 - paired-end sequencing dataset of dental calculus from chimpanzees.

• Fastq files 2 - paired-end sequencing dataset of dental calculus from ancient humans (for further practice).

• Kraken2 2Gb database - built from complete genomes of bacteria, archaea, fungi and protozoa in the NCBI RefSeq.

• Scripts used during the course.

To practice some of the most used command lines in Linux we will go through a tutorial by Kristian Rother (Academis). Download and follow the instructions step-by-step to find the hidden word.