marinetics - Alexander Jueterbock Website

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PhD course
High throughput sequencing of non-model organisms

Course material for bioinformatics data analysis

Alexander Jueterbock

Martin Jakt

Recommended links and literature

Materials

Prerequisites

RADseq lecture

Introduction to bioinformatics

Unix tools

Trimming and Quality control

Genome assembly

Mapping and Variant Calling

Links

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The following sections list relevant literature, links to analysis pipelines, as well as to tutorials and learning environments that get you closer to become bioinformatics-experts.

Recommended Reading for RAD sequencing

Baird, Nathan A., et al. “Rapid SNP discovery and genetic mapping using sequenced RAD markers.” PloS one 3.10 (2008): e3376.

Baker, Monya. “De novo genome assembly: what every biologist should know.” Nature methods 9.4 (2012): 333-337

Catchen, Julian, et al. “Stacks: an analysis tool set for population genomics.” Molecular ecology 22.11 (2013): 3124-3140.

DaCosta, Jeffrey M., and Michael D. Sorenson. “Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol.” PloS one 9.9 (2014): e106713.

Davey, John W., and Mark L. Blaxter. “RADSeq: next-generation population genetics.” Briefings in Functional Genomics 9.5-6 (2010): 416-423.

Hohenlohe, Paul A., et al. “Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.” PLoS genetics 6.2 (2010): e1000862.

Hohenlohe, Paul A., et al. “Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout.” Molecular ecology resources 11.s1 (2011): 117-122.

Peterson, Brant K., et al. “Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species.” PloS one 7.5 (2012): e37135.

Rasic, Gordana, et al. “Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti.” BMC genomics 15.1 (2014): 275.

Schweyen, Hannah, Andrey Rozenberg, and Florian Leese. “Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters.” The Biological Bulletin 227.2 (2014): 146-160.

Puritz, Jonathan B., Christopher M. Hollenbeck, and John R. Gold. “dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.” PeerJ 2 (2014): e431.

Puritz, Jonathan B., et al. “Demystifying the RAD fad.” Molecular ecology 23.24 (2014): 5937-5942.

Blog on RAD seq

Guidelines for pooled sequencing data

Schlotterer, Christian, et al. “Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.” Nature Reviews Genetics (2014).

Useful programs and analysis pipelines

Popoolation: Population genomic analysis of pooled samples, see also this presentation

Popoolation 2: allows comparison of allele frequencies between two or more populaitons

The Simple Fool’s Guide to Population Genomics via RNA-Seq

Bioconductor: R packages for genomic data analysis

Rosalind: Learning python

Biopython

BioPerl

STACKS: building loci from short sequences and analyzing RADseq data

Ddocent: ddRAD analysis pipeline

Upcoming Coursera courses

R programming

Algorithms, Biology, and Programming for Beginners

Epigenetic Control of Gene Expression

Bioconductor for Genomic Data Science

Statistics for Genomic Data Science

Comparing Genes, Proteins, and Genomes (Bioinformatics III)

Python for Genomic Data Science

Command Line Tools for Genomic Data Science