VGP assembly: training workflow 4.0
Visit source
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
VGP assembly tutorial
Associated Tutorial
This workflows is part of the tutorial Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step, available in the GTN
Thanks to...
Tutorial Author(s): Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Anna Syme, Linelle Abueg, Brandon Pickett, Giulio Formenti, Marcella Sozzoni, Anton Nekrutenko
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bionano_dataset | Bionano_dataset | n/a |
|
| Hi-C_dataset_F | Hi-C_dataset_F | n/a |
|
| Hi-C_dataset_R | Hi-C_dataset_R | n/a |
|
| Input Dataset Collection | Input Dataset Collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 5 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 6 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2 |
| 7 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 8 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 9 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 10 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 11 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4 |
| 12 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 13 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4 |
| 14 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 15 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4 |
| 16 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 17 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4 |
| 18 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1 |
| 19 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 20 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 |
| 21 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 22 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
| 23 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 24 | Bionano Hybrid Scaffold | toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0 |
| 25 | Concatenate datasets | cat1 |
| 26 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 27 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
| 28 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 29 | Concatenate datasets | cat1 |
| 30 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 31 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 32 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 33 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
| 34 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
| 35 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 36 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 37 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 |
| 38 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4 |
| 39 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 40 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 41 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 42 | Convert | Convert characters1 |
| 43 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0 |
| 44 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 45 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
| 46 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 |
| 47 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0 |
| 48 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 |
| 49 | Sort | sort1 |
| 50 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1 |
| 51 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 52 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4 |
| 53 | SALSA | toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2 |
| 54 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 55 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 56 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 57 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4 |
| 58 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0 |
| 59 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0 |
| 60 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1 |
Version History
master
Creators and Submitter
Discussion Channel
Activity
Views: 1178 Downloads: 160 Runs: 4
Created: 2nd Jun 2025 at 11:00
AttributionsNone
Related items
Advanced People list for this Workflow with search and filtering
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Advanced Spaces list for this Workflow with search and filtering
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
Advanced Teams list for this Workflow with search and filtering
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
