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
Transcriptomics
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- Computational methods for transcriptome annotation and quantification using RNA-seq
- De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
- Trinotate: Functional annotation of transcripts
- Genome-wide mapping of in vivo protein-DNA interactions
Genome Assembly
- Overview and comparison of assembly algorithms
- Genome assembler benchmarks (scroll down)
- Assemblathon 2 comparison of denovo assembly algorithms
- SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
- De novo transcriptome assembly with ABySS
- Velvet: algorithms for de novo short read assembly using de Bruijn graphs
Genome Structure Variation
- Genome structural vatiants in human diseases
- Mapping copy number variation by population-scale genome sequencing
Metagenomics
- A Primer on Metagenomics
- Next-generation sequencing technologies for environmental DNA research
- Sequencing our way towards understanding global eukaryotic biodiversity
- QIIME allows analysis of high-throughput community sequencing data
- 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