Assembly-Hifi-only-VGP3/main
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Workflow Type: Galaxy
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Tests Contiging Solo:
Generate assembly based on PacBio Hifi Reads.
Inputs
- Hifi long reads [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
- Genomescope Model Parameters generated by Genomescope [tabular]
- Database for busco lineage (recommended: latest)
- Busco lineage (recommended: vertebrata)
- Name of first assembly
- Name of second assembly
Outputs
- Primary assembly
- Alternate assembly
- QC: Bandage image for the raw unitigs
- 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. |
|
| Database for Busco Lineage | Database for Busco Lineage | n/a |
|
| Genomescope Model Parameters | Genomescope Model Parameters | GenomeScope model parameters generated by K-mer profiling workflow |
|
| Genomescope Summary | Genomescope Summary | n/a |
|
| Homozygous Read Coverage | Homozygous Read Coverage | If empty, read coverage will be estimated from the Genomescope parameters. |
|
| Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis |
|
| 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 |
|---|---|---|
| 11 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 12 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 13 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 14 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 15 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1 |
| 16 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 17 | Cut | Cut1 |
| 18 | Convert | Convert characters1 |
| 19 | Parse parameter value | param_value_from_file |
| 20 | Cut | Cut1 |
| 21 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 22 | Estimated genome size | param_value_from_file |
| 23 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0 |
| 24 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 25 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 26 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 27 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 29 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 30 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2 |
| 33 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0 |
| 34 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 35 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 36 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 37 | Data Prep Primary | n/a |
| 38 | Data Prep Alternate | n/a |
| 39 | merqury_qv | __EXTRACT_DATASET__ |
| 40 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 41 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 42 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 43 | merqury_stats | __EXTRACT_DATASET__ |
| 44 | Join two Datasets | join1 |
| 45 | Plotting Nx and Sizes | n/a |
| 46 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2 |
| 47 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| multiqc html report | multiqc html report | n/a |
|
| cutadapt multiqc stats | cutadapt multiqc stats | n/a |
|
| Estimated Genome size | Estimated Genome size | n/a |
|
| Hifiasm Alternate gfa | Hifiasm Alternate gfa | n/a |
|
| Hifiasm Primary gfa | Hifiasm Primary gfa | n/a |
|
| raw unitig graph image | raw unitig graph image | n/a |
|
| Usable GFA Alternate | Usable GFA Alternate | n/a |
|
| Usable GFA Primary | Usable GFA Primary | n/a |
|
| Hifiasm Primary assembly | Hifiasm Primary assembly | n/a |
|
| Hifiasm Alternate assembly | Hifiasm Alternate assembly | 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 |
|
| Busco Summary | Busco Summary | n/a |
|
| Busco summary image | Busco summary image | n/a |
|
| Merqury png | Merqury png | n/a |
|
| Merqury Histograms | Merqury Histograms | n/a |
|
| Merqury completeness stats | Merqury completeness stats | n/a |
|
| merqury_qv | merqury_qv | n/a |
|
| output_merqury.spectra-cn.fl | output_merqury.spectra-cn.fl | n/a |
|
| output_merqury.spectra-asm.fl | output_merqury.spectra-asm.fl | n/a |
|
| output_merqury.assembly_01.spectra-cn.fl | output_merqury.assembly_01.spectra-cn.fl | n/a |
|
| merqury_stats | merqury_stats | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Assembly statistics | Assembly statistics | n/a |
|
| clean_stats | clean_stats | 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: 24516 Downloads: 127540 Runs: 19
Created: 20th Oct 2023 at 03:01
Last updated: 15th Mar 2026 at 03:01
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