RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

• RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

• RepeatMasker is a program that analyzes ...

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.

This workflow uses eggNOG mapper and InterProScan for functional annotation of protein sequences.

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.

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 ...

The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.

Associated Tutorial

This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN

Features

• Includes [Galaxy Workflow ...

This workflow uses Braker3 to annotate a genome.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Braker3, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...