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Introduction to R

Lectures Lecture1_2017 Lecture2_2017 Tutorial instructions: Lab1_R_2017 Lab2_R_2017 Files need for Extra R-exercises: clinic_file One day R-Exercises Bioinformatics_Course <a href=”http://77.235.253.122/tutorials/courses_data/gapminder-FiveYearData.csv

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Metagenome Assembly

Metagenome Assembly In this tutorial you’ll learn how to inspect the quality of High-throughput sequencing and perform a metagenomic assembly. We will use data under the accession SRS018585 in the Sequence Read Archive. this sample is “a Human Metagenome sample

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Whole Metagenome Sequencing

In this tutorial we will compare samples from the Pig Gut Microbiome to samples from the Human Gut Microbiome. Whole Metagenome sequencing (WMS), or shotgun metagenome sequencing, is a relatively new and powerful sequencing approach that provides insight into community

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16s Metabarcoding Analysis

This tutorial is largely inspired of the MiSeq SOP from the Schloss Lab. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the

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RNA-Seq analysis

Downloading the data For this tutorial we will use the test data from this paper: Malachi Griffith*, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith*. 2015. Informatics for RNA-seq: A web resource for analysis on the

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Pan-genome analysis

In this tutorial we will learn how to determine a pan-genome from a collection of isolate genomes. This tutorial is inspired from Genome annotation and Pangenome Analysis from the CBIB in Santiago, Chile

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Mapping and variant calling

In this practical you will learn to map NGS reads to a reference sequence, check the output using a viewer software and investigate some aspects of the results. You will be using the read data from the Quality Control practical.

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Genome Annotation with Prokka

After you have de novo assembled your genome sequencing reads into contigs, it is useful to know what genomic features are on those contigs. The process of identifying and labelling those features is called genome annotation. Prokka is a “wrapper”;

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