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Introduction to UNIX

This tutorial is largely inspired of the Introduction to UNIX course from the Sanger Institute. The aim of this module is to introduce Unix and cover some of the basics that will allow you to be more comfortable with the

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Introduction to programming

The aim of this module is to present you with an introduction to programming, guiding you through useful Unix commands and essential programming concepts. The first part of this module introduces you to more advanced Unix concepts, illustrating these concepts

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Introduction to Ugene

UGENE is a free cross-platform software bioinformatics software. UGENE integrates dozens of well-known bioinformatics tools and algorithms available both through the GUI or through the command line. UGENE Workflow Designer is a central part of UGENE that allows a molecular biologist

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NGS analysis with Galaxy

The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data and to cope with this we need systems to help us analyze this data. In this module we will introduce you to

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Genome analysis with Artemis

The aim of this Module is for you to become familiar with the basic functions of Artemis using a series of worked examples. These examples are designed to take you through the most immediately useful functions. However, there will be

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Mapping short reads

In this module, we will introduce to you the biology and the Workflow, mapping software, SAMtools, SAM/BAM and FASTQ file format. After we will show how Next Generation Sequencing data can be viewed in Artemis alongside your chosen reference using

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Genome assembly

One of the greatest challenges of sequencing a genome is determining how to arrange sequencing reads into chromosomes. This process of determining how the reads fit together by looking for overlaps between them is called genome assembly. Capillary sequencing reads

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Genome annotation

The aims of this module is to introduce how generate an initial set of gene models (merging RATT and Augustus), how map RNA-Seq data to a reference and viewing RNA-Seq mapping in Artemis. We will show how correcting gene models

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Comparative genomics

The aim of this Module is for you to become familiar with the basic functions of ACT by using a series of worked examples. Some of these examples will touch on exercises that were used in previous Modules, this is

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GWAS (Plink)

The goal of this module will be to introduce you to run a GWAS on a dataset for an SLE-related disease in dogs by using PLINK, to visualize the results with a Manhattan plot, to look at stratification structure within

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File Formats

This lecture is aimed at making you discover the most popular file formats used in bioinformatics. You’re expected to have basic working knowledge of Linux to be able to follow the lesson.

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Quality control

In this practical you will learn to import, view and check the quality of NGS read data in FASTQ format. You will be working with an Illumina MiSeq read dataset from a genome sequence project. The sequenced organism is an

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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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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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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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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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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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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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