Tutorials and useful links
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!
- 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.
- Comprative genomics tutorials
- Long-read sequencer comparison
- CAFE tutorial for gene family evolution
- 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!
- 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
- 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
- Comprehensive list of DNA-Methylationmethods, tools, pitfalls, tutorials, pipelines, packages
- 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
- Establishing a laboratory book for new PIs