Scaffolding-HiC-VGP8/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Scaffolding using HiC data with YAHS.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Database for Busco Lineage | Database for Busco Lineage | n/a |
|
| Estimated genome size - Parameter File | Estimated genome size - Parameter File | Estimated genome size from contiging workflow |
|
| Haplotype | Haplotype | n/a |
|
| HiC Forward reads | HiC Forward reads | Forward reads as a single dataset in fastq format |
|
| HiC reverse reads | HiC reverse reads | Reverse reads as a single dataset in fastq format |
|
| Input GFA | Input GFA | The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. |
|
| Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis |
|
| Restriction enzymes | Restriction enzymes | Restriction enzymes used in preparation of Hi-C libraries. |
|
| SAK input file | SAK input file | n/a |
|
| Sequence graph | Sequence graph | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 11 | Parse parameter value | param_value_from_file |
| 12 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 13 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 14 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 15 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
| 16 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 17 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2 |
| 18 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
| 19 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 20 | Extract dataset | __EXTRACT_DATASET__ |
| 21 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 22 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 23 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 24 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 25 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 26 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 27 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 28 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 29 | gfastats_data_prep | n/a |
| 30 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
| 31 | Cut | Cut1 |
| 32 | Cut | Cut1 |
| 33 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 34 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0 |
| 35 | Nx Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
| 36 | Size Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
| 37 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
| 38 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1 |
| 39 | Extract dataset | __EXTRACT_DATASET__ |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| YAHS on input dataset(s): Final scaffolds agp output | YAHS on input dataset(s): Final scaffolds agp output | n/a |
|
| Pretext Map Before HiC scaffolding | Pretext Map Before HiC scaffolding | n/a |
|
| Reconciliated Scaffolds: gfa | Reconciliated Scaffolds: gfa | n/a |
|
| Reconciliated Scaffolds: fasta | Reconciliated Scaffolds: fasta | n/a |
|
| Assembly Statistics for s2 | Assembly Statistics for s2 | n/a |
|
| Scaffold sizes for s2 | Scaffold sizes for s2 | n/a |
|
| Busco Summary | Busco Summary | n/a |
|
| Busco Summary image | Busco Summary image | n/a |
|
| clean_stats | clean_stats | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Pretext Map After HiC scaffolding | Pretext Map After HiC scaffolding | n/a |
|
Version History
v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.195a269d
Creators and Submitter
Activity
Views: 27336 Downloads: 148741 Runs: 10
Created: 27th Oct 2023 at 03:01
Last updated: 12th Mar 2026 at 03:01
Annotated Properties
Scientific disciplines
Computer Science
TagsThis item has not yet been tagged.
AttributionsNone
Related items
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 Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
