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
Text-mining exercises
Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.
Scientific topics: Data mining, Natural language processing, Metagenomics, Microbial ecology
Text-mining exercises
http://jensenlab.org/training/textmining/
http://tess.elixir-uk.org/materials/text-mining-exercises
Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.
Evangelos Pafilis
Lars Juhl Jensen
Manimozhiyan Arumugam
Data mining
Natural language processing
Metagenomics
Microbial ecology
Bioinformaticians
Biologists
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
