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This repository contains course materials for a workshop on structural genome annotation with BRAKER and TSEBRA
Authors
Genome annotation
Days since last push
477
day(s)
2023-11-22
License
GNU General Public License v3.0
By the end of this session you will be able to:
Understand the main uses of BUSCO in genomics
Understand how BUSCO operates behind the scenes
Run example assessments of genomic data with BUSCO
Navigate your way around the main BUSCO outputs
Assembly Evaluation
Genome annotation
Days since last push
534
day(s)
2023-09-26
License
MIT License
By the end of this session, you will be able to:
Structurally and functionally annotate a eukaryotic genome assembly with EASEL using protein and RNA extrinsic evidence
Assess non-model genome annotation quality with BUSCO score, mono:multi-exonic ratio, and reciprocal BLAST annotation rate
Address challenges with accuracy and efficiency for genome annotation
Genomics
Transcriptomics
Days since last push
573
day(s)
2023-08-18
License
MIT License
Authors
Hadrien Gourlé, Juliette Hayer, Oskar Karlsson, Jacques Dainat
High performance computing
Genomics
Genome assembly
Genome annotation
Next generation sequencing
Days since last push
-
License
Creative Commons Attribution 4.0
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Authors
Anthony Bretaudeau
Genome annotation
Galaxy
Days since last push
-
License
Creative Commons Attribution 4.0
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Authors
Anthony Bretaudeau
Galaxy
Genome annotation
Days since last push
-
License
Creative Commons Attribution 4.0
Authors
Yannis Nevers
Genomics
Genome annotation
Comparative genomics
Days since last push
-
License
Standard Youtube License
Authors
Emily Perry
Benjamin Moore
Helen Sparrow
Giulietta M. Spudich
Aleena Mushtaq
Genome annotation
Database Management
Days since last push
-
License
Creative Commons Attribution 4.0
RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multip...
Authors
Dr Nandan Deshpande
RNA-seq
Next generation sequencing
Genome annotation
Days since last push
-
License
Creative Commons Attribution 4.0
Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.
Authors
Anthony Bretaudeau, Helena Rasche, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Genome annotation
Galaxy
Genomics
Days since last push
-
License
Creative Commons Attribution 4.0
Rfam is a database of RNA families that currently contains over 4,000 families. Together with the Infernal software, Rfam is commonly used to annotate non-coding RNAs in newly sequenced genomes.
This webinar gives an overview of the data available in Rfam and give a live demo of annotating a genome with non-coding RNAs using Rfam and the Infernal software.
Authors
Emma Cooke, Nancy Ontiveros, Blake Sweeney, Sam Griffiths-Jones
Genome annotation
Genomics
Database Management
Days since last push
-
License
Creative Commons Attribution 4.0
A walk-through of a manual curation technique for genome assembly
Authors
Camilla Ryan
Genome assembly
Assembly Curation
Genomics
Days since last push
-
License
-
Authors
Leanne Haggerty
Swati Sinha
Swati Sinha
Genome annotation
Days since last push
-
License
Standard Youtube License
An introduction and summary of Earl Grey - A user-friendly and fully automated TE annotation pipeline to steamline TE curation and annotation in diverse geno...
Authors
Tobias Baril
Genomics
Genome annotation
Days since last push
-
License
Standard Youtube License
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Authors
Romane Libouban, Anthony Bretaudeau
Genomics
Galaxy
Genome annotation
Days since last push
-
License
Creative Commons Attribution 4.0
Thorough guide for annotating and masking repeats using RepeatModeler/RepeatMasker.
Authors
Daren Card
Genome annotation
Days since last push
-
License
MIT License
Authors
Genomics
Data management
Data submission
Variant analysis
Transcriptomics
FAIR data
Assembly Evaluation
Days since last push
-
License
Creative Commons Attribution 4.0
Every year, the students attending Introduction to Bioinformatics have the opportunity to listen to experts working in this field.In the second session, Tyle...
Authors
Tyler Alioto
Genomics
Genome annotation
Genome assembly
Days since last push
-
License
Standard Youtube License
Topics