Tutorials and useful links

(Updated 30/03/2022)

General genomics (sequencing, lib prep, extraction)

• Excellent tutorials on every flavor of genomics
• Info on Pacbio’s Sequel II
• Extracting long-read DNA for Pacbio
• Starting with Genomics, unix and programming? Look no further, Ming Tang has compiled a comprehensive list of resources
• Sequence file formats
• Catalogue of long-read tools
• Tons of one liners to modify genomic files!

Population Genomics

• PCA, STRUCTURE, SNAPP - Some of my scripts
• ABBA-BABA synthesis and plot
• List of tutorials in speciation genomics by Mark Ravinet and Joana Meier
• List of programs in populations genomics using genomic-level data
• List of tutorials included Evomics course on Speciation and Population Genomics 2016 and 2018 tutorials - including ABBA-BABA, FasSimCoal, PCA, STRUCTURE
• SNP-filtering tutorial by Jonathan Puritz
• Book on population genomics with code and exercises
• Have not yet tested, but maybe a practical way to run D-statistics from a VCF
• Variant-calling tutorial
• Needing some help with GATK for non-model organisms?
• Mark Ravinet has a three part tutorial on how to detect selection! See part 1 here, part 2 here, and part 3 here.
• Brilliant tutorial on hybridization/introgression
• Brilliant tutorial on low-coverage data / ANGSD

Comparative Genomics

• Check our Kmer tutorials
• Repeat annotation of genomes, by the brilliant Clemént Goubert
• Comprative genomics tutorials
• Long-read sequencer comparison
• Repeat annotation in genomes
• Trying to estimate plody-level with the GenomeScope-Smudgeplot combo, but are getting weird results? Kamil Jaron has a bunch to show you
• Handling GTF, GFF, GFF3 files
• How to run and interpret OrthoFinder
• Retrieving Homologous Chromossomic regions and plotting it
• Excellent tutorial on genome repeat and TE annotation
• Promising list of tutorials with CoGe to find features in your genome.
• Two ways of making better use of RepeatMasker to build RepeatLibraries. See here and here.
• This program looks like an easy way to look for synteny!

Phylogenomics

• List of tutorials on phylogenetic inference by Michael Matschiner
• Tutorials on phylogenomics included in the Evomics course 2016 and 2018 tutorials
• Really good tree handling and plotting examples
• Phylogenies with vcftools? Maybe try SNPphylo

RNA-Seq

• Mind-blowing list of RNA-seq methods, tools, pitfalls, tutorials, pipelines, packages
• RNA-Seq tutorial
• RNA-Seq ‘genome browser’
• RNA-Seq tutorial
• RNA-Seq basics, and pipeline overview

Methylation

• Comprehensive list of DNA-Methylationmethods, tools, pitfalls, tutorials, pipelines, packages

Evolutionary Biology

• Easily broken down statistics for biologists!

Data Visualization (R, python)

• Pathwork, an interesting way to combine plots
• Something I want to explore better, plotly for R and python
• The usual suspect, ggplot2

Career-oriented

• Establishing a laboratory book for new PIs