Assembly-Hifi-only-VGP3/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Frozen
Tests Contiging Solo w/HiC:
Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.
Inputs
- Hifi long reads [fastq]
- HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
- HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Name of first assembly
- Name of second assembly
Outputs
- Haplotype 1 assembly
- Haplotype 2 assembly
- QC: BUSCO report for both assemblies
- QC: Merqury report for both assemblies
- QC: Assembly statistics for both assemblies
- QC: Nx plot for both assemblies
- QC: Size plot for both assemblie
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bits for Hifiasm bloom filter | Bits for Hifiasm bloom filter | Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting. |
|
| Genomescope Summary | Genomescope Summary | n/a |
|
| Meryl Database | Meryl Database | n/a |
|
| Name of alternate assembly | Name of alternate assembly | n/a |
|
| Name of primary assembly | Name of primary assembly | n/a |
|
| Pacbio Reads Collection | Pacbio Reads Collection | n/a |
|
| SAK input file (Optional) | SAK input file (Optional) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0 |
| 8 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 9 | Pick parameter value | pick_value |
| 10 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 11 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
| 12 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1 |
| 13 | Convert | Convert characters1 |
| 14 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 15 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 16 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 17 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 18 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 19 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 20 | Cut | Cut1 |
| 21 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 22 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3 |
| 23 | Data Prep Primary | n/a |
| 24 | Data Prep Alternate | n/a |
| 25 | Estimated genome size | param_value_from_file |
| 26 | Plotting Nx and Sizes | n/a |
| 27 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 29 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 30 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 31 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| cutadapt multiqc stats | cutadapt multiqc stats | n/a |
|
| multiqc html report | multiqc html report | n/a |
|
| Hifiasm Primary gfa | Hifiasm Primary gfa | n/a |
|
| Hifiasm Alternate gfa | Hifiasm Alternate gfa | n/a |
|
| Usable GFA Primary | Usable GFA Primary | n/a |
|
| Usable GFA Alternate | Usable GFA Alternate | n/a |
|
| Hifiasm Primary assembly | Hifiasm Primary assembly | n/a |
|
| Hifiasm Alternate assembly | Hifiasm Alternate assembly | n/a |
|
| Busco summary image | Busco summary image | n/a |
|
| Merqury png | Merqury png | n/a |
|
| Merqury completeness stats | Merqury completeness stats | n/a |
|
| Merqury Histograms | Merqury Histograms | n/a |
|
| Estimated Genome size | Estimated Genome size | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Assembly Stats on Primary assembly | Assembly Stats on Primary assembly | n/a |
|
| Assembly Stats on Alternate Assembly | Assembly Stats on Alternate Assembly | n/a |
|
| Assembly statistics | Assembly statistics | n/a |
|
Version History
v0.3.5 (latest) Created 15th Mar 2026 at 03:01 by WorkflowHub Bot
Updated to v0.3.5
Frozen
v0.3.568cfba6
v0.1 (earliest) Created 20th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
1f63570
Creators and Submitter
Activity
Views: 26343 Downloads: 151709 Runs: 19
Created: 20th Oct 2023 at 03:01
Last updated: 15th 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/
