Assembly - Making sense of a newly assembled genome
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Making sense of a newly assembled genome
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html
http://tess.elixir-uk.org/materials/assembly-making-sense-of-a-newly-assembled-genome
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?
Objectives of the tutorial:
- Identification of the most closely related genome to my new assembly
- Perform sequence comparison to locate rearrangements
- Identify genes located in deletions
nekrut
delphine-l
Assembly - Unicycler Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Unicycler Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-unicycler-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I have short reads and long reads. How do I assemble a genome?
Objectives of the tutorial:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with Prokka
nekrut
delphine-l
slugger70
Assembly - De Bruijn Graph Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - De Bruijn Graph Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-de-bruijn-graph-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- What are the factors that affect genome assembly?
- How does Genome assembly work?
Objectives of the tutorial:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly using the SPAdes assembler.
slugger70
Assembly - Introduction to Genome Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Introduction to Genome Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
http://tess.elixir-uk.org/materials/assembly-introduction-to-genome-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- How do we perform a very basic genome assembly from short read data?
Objectives of the tutorial:
- assemble some paired end reads using Velvet
- examine the output of the assembly.
slugger70
Metagenomics - Analyses of metagenomics data - The global picture
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- How to analyze metagenomics data?
- What information can be extracted of metagenomics data?
- What is the difference between amplicon and shotgun data?
- What are the difference...
Metagenomics - Analyses of metagenomics data - The global picture
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html
http://tess.elixir-uk.org/materials/metagenomics-analyses-of-metagenomics-data-the-global-picture
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- How to analyze metagenomics data?
- What information can be extracted of metagenomics data?
- What is the difference between amplicon and shotgun data?
- What are the difference in the analyses of amplicon and shotgun data?
Objectives of the tutorial:
- Choosing the best approach to analyze metagenomics data
- Selection of tools to analyze amplicon data or shotgun data
- Visualisation of a community structure
shiltemann
bebatut
Metagenomics - 16S Microbial Analysis with Mothur
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- What is the effect of normal variation in the gut microbiome on host health?
Objectives of the tutorial:
- Analyze of 16S rRNA sequencing data using the Mothur toolsuite in...
Metagenomics - 16S Microbial Analysis with Mothur
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
http://tess.elixir-uk.org/materials/metagenomics-16s-microbial-analysis-with-mothur
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- What is the effect of normal variation in the gut microbiome on host health?
Objectives of the tutorial:
- Analyze of 16S rRNA sequencing data using the Mothur toolsuite in Galaxy
shiltemann
bebatut
