Module: Genome Assembly

This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.

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• assemble some paired end reads using Velvet
• examine the output of the assembly.

In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.

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• Assemble a chloroplast genome from long reads
• Polish the assembly with short reads
• Annotate the assembly and view
• Map reads to the assembly and view

In this tutorial, we will walk you through an assembly of a large genome, such as a plant or animal genome.

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• Assemble a large genome from long reads
• Polish the assembly
• Assess the quality of the assembly

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.

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• Describe what an assembly is
• Describe what de-replication is
• Explain the difference between co-assembly and individual assembly
• Explain the difference between reads, contigs and scaffolds
• Explain how tools based on De Bruijn graph work
• Apply appropriate tools for analyzing the quality of metagenomic data
• Construct and apply simple assembly pipelines on short read data
• Apply appropriate tools for analyzing the quality of metagenomic assembly
• Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome

This tutorial guides you through the preprocessing of sequencing data of bronchoalveolar lavage fluid (BALF) samples obtained from early COVID-19 patients in China. Since such samples are expected to be contaminated signficantly with human sequenced reads, the goal is to enrich the data for SARS-CoV-2 reads by identifying and discarding reads of human origin before trying to assemble the viral genome sequence.

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This demo walks you through running the VGP Genome Assembly workflows, rather than the whole tutorial (as most GTN videos do)

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• Non-GTN Lecture

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