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Authors: Jared Simpson  or Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or nekrut  or Boris Steipe 


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...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome https://tess.elixir-europe.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
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,...

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems https://tess.elixir-europe.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.
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...

Resource type: Tutorial

Assembly - Unicycler Assembly https://tess.elixir-europe.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