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
Variant Analysis - Calling variants in non-diploid systems
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How does frequency of mitochondrial polymorphisms change from mother to child?
Objectives of the tutorial:
- Using Galaxy's main site we will see how to call variants in bacteria,...
Variant Analysis - Calling variants in non-diploid systems
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html
http://tess.elixir-uk.org/materials/variant-analysis-calling-variants-in-non-diploid-systems
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How does frequency of mitochondrial polymorphisms change from mother to child?
Objectives of the tutorial:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
nekrut
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
