Want to read up and try out things ahead of the workshop?
Below we’ve put a couple of useful resources you could check out prior to the workshop. We’ll start from scratch in the workshop tutorials, so don’t worry if you don’t have the time to familiarize yourself with everything.
Starting point
Unix and R
- Interactive tutorials for exploring bioinformatics command-line tools in a secure sandbox
- UNIX cheat sheet (example)
- Unix and Perl for Biologists (Unix part)
- An Introduction to R in R (fun interactive tutorial: swirl)
- R for data science (excellent free book)
- R tidyverse cheat sheets
Modern Genome Sequencing Technology
the technologies emerge, develop and improve so fast that this section can never be up-to-date
- Towards population-scale long-read sequencing
- Advancements in Next-Generation Sequencing
- Coming of age: ten years of next-generation sequencing technologies
- The impact of next-generation sequencing technology on genetics
- Bioinformatics for High Throughput Sequencing
- The Principles and Applications of High-Throughput Sequencing Technologies
- Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
- Next-generation data filtering in the genomics era
Transcriptomics
- Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
- A simple guide to de novo transcriptome assembly and annotation
- De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
- Trinotate: Functional annotation of transcripts
Genome Assembly
- Genome assembly in the telomere-to-telomere era
- The present and future of de novo whole-genome assembly
- A comprehensive review of scaffolding methods in genome assembly
- New approaches for genome assembly and scaffolding
- Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
- RepeatModeler2 for automated genomic discovery of transposable element families
Genome Structure Variation
- A roadmap for understanding the evolutionary significance of structural genomic variation
- Genome structural vatiants in human diseases
- Mapping copy number variation by population-scale genome sequencing
Metagenomics
- Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
- What Is Metagenomics Teaching Us, and What Is Missed?
- QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
- High-quality metagenome assembly from long accurate reads with metaMDBG
- metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
- Sequencing our way towards understanding global eukaryotic biodiversity
- Supervised classification of human microbiota
- Classification Resources for Environmental Sequence Tags
- Removing noise from pyrosequenced amplicons
- Evaluation of 16S rDNA-based community profiling for human microbiome research
Single Cell Sequencing
- Methods and applications for single-cell and spatial multi-omics
- Single-cell genome sequencing: current state of the science
- The technological landscape and applications of single-cell multi-omics
Pan-genome
Blogs, Newsletters, and (free) Courses
- The Missing Semester of Your CS Education
- Modern Plain Text Computing
- File Not Found – GenZ and filesystems
- Speciation & Population Genomics: a how-to-guide
- omic.ly – A weekly newsletter on omics and clinical laboratory diagnostics
- Getting started with genomics tools and resources newsletter
- Tutorials for analysis of low-coverage whole genome sequencing data