Refining Genome Annotations with Apollo

Associated Tutorial

This workflows is part of the tutorial Refining Genome Annotations with Apollo (prokaryotes), available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau, [Helena ...

Genome annotation with Maker (short)

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Maker (short), available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau

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A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER

Associated Tutorial

This workflows is part of the tutorial From small to large-scale genome comparison, available in the GTN

Thanks to...

Tutorial Author(s): Esteban Perez-Wohlfeil ...

A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment

Associated Tutorial

This workflows is part of the tutorial From small to large-scale genome comparison, available in the GTN

Thanks to...

Tutorial Author(s): Esteban Perez-Wohlfeil ...

Masking repeats in a genome using RepeatMasker

Associated Tutorial

This workflows is part of the tutorial Masking repeats with RepeatMasker, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Anthony ...

CRISPR screen analysis

Associated Tutorial

This workflows is part of the tutorial CRISPR screen analysis, available in the GTN

Thanks to...

Tutorial Author(s): Maria Doyle, Kenji Fujihara, ...

Essential genes detection with Transposon insertion sequencing

Associated Tutorial

This workflows is part of the tutorial Essential genes detection with Transposon insertion sequencing, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

...

Structural and functional genome annotation with Funannotate

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Funannotate, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

**Workflow ...

Functional annotation of protein sequences

Associated Tutorial

This workflows is part of the tutorial Functional annotation of protein sequences, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): ...

Workflows for comparison of genes in annotated genomes

Associated Tutorial

This workflows is part of the tutorial Comparative gene analysis in unannotated genomes, available in the GTN

Thanks to...

Workflow Author(s): Anton Nekrutenko

Tutorial Author(s): Anton Nekrutenko ...

Bacterial Genome Annotation

Associated Tutorial

This workflows is part of the tutorial Bacterial Genome Annotation, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Bérénice Batut, ...

Genome annotation with Maker

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Maker, available in the GTN

Thanks to...

Workflow Author(s): Anthony Bretaudeau, French National Institute for Agriculture, Food, and Environment (INRAE)

Tutorial Author(s): [Anthony ...

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Helixer, available ...

Genome annotation with Prokka

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Prokka, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Anna Syme, Torsten ...

Identification of AMR genes in an assembled bacterial genome

Associated Tutorial

This workflows is part of the tutorial Identification of AMR genes in an assembled bacterial genome, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Associated Tutorial

This workflows is part of the tutorial Long non-coding RNAs (lncRNAs) annotation with FEELnc, available in the GTN

Thanks to...

Workflow Author(s): Stéphanie Robin

Tutorial Author(s): Stéphanie Robin ...

CWL4IncorporateTSSintoGXF

This ...

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

• pomoxis assess_assembly and assess_homopolymers
• dnadiff from the mummer package
• NucDiff
• QUAST
• BUSCO

...

Functional annotation of protein sequences

Structural and functional genome annotation with Funannotate

Masking repeats in a genome using RepeatMasker

Refining Genome Annotations with Apollo