Assembly-Hifi-only-VGP3/main
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Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly Name | Assembly Name | For workflow report. |
|
| 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 |
|
| Species Name | Species Name | For workflow report. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 12 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 13 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 14 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 15 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2 |
| 16 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 17 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 18 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 19 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 20 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2 |
| 21 | Cut | Cut1 |
| 22 | Convert | Convert characters1 |
| 23 | Parse parameter value | param_value_from_file |
| 24 | Cut | Cut1 |
| 25 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 26 | Estimated genome size | param_value_from_file |
| 27 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
| 28 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 29 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 30 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 33 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 34 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 36 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 37 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 38 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 39 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 40 | compleasm | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 41 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 42 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 43 | compleasm | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 44 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 45 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 46 | Data Prep Primary | n/a |
| 47 | Data Prep Alternate | n/a |
| 48 | merqury_qv | __EXTRACT_DATASET__ |
| 49 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 50 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 51 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 52 | merqury_stats | __EXTRACT_DATASET__ |
| 53 | Join two Datasets | join1 |
| 54 | Plotting Nx and Sizes | n/a |
| 55 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2 |
| 56 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Species Name for report | Species Name for report | n/a |
|
| Assembly Name for report | Assembly Name for report | n/a |
|
| Lineage for report | Lineage for report | n/a |
|
| 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 Primary gfa | Hifiasm Primary gfa | n/a |
|
| Hifiasm Alternate gfa | Hifiasm Alternate gfa | n/a |
|
| raw unitig graph image | raw unitig graph image | n/a |
|
| Usable GFA Primary | Usable GFA Primary | n/a |
|
| Usable GFA Primary no sequences | Usable GFA Primary no sequences | n/a |
|
| Usable GFA Alternate | Usable GFA Alternate | n/a |
|
| Usable GFA Alternate no sequences | Usable GFA Alternate no sequences | 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 |
|
| Compleasm on Primary Assembly contigs: Full table Busco | Compleasm on Primary Assembly contigs: Full table Busco | n/a |
|
| Compleasm on Primary Assembly contigs: Full table | Compleasm on Primary Assembly contigs: Full table | n/a |
|
| Compleasm on Primary Assembly contigs: Miniprot | Compleasm on Primary Assembly contigs: Miniprot | n/a |
|
| Compleasm on Primary Assembly contigs: Translated Proteins | Compleasm on Primary Assembly contigs: Translated Proteins | n/a |
|
| Merqury Histograms | Merqury Histograms | n/a |
|
| Merqury png | Merqury png | n/a |
|
| Merqury completeness stats | Merqury completeness stats | n/a |
|
| Busco Summary Alt | Busco Summary Alt | n/a |
|
| Busco summary image Alt | Busco summary image Alt | n/a |
|
| Compleasm on Alternate Assembly contigs: Miniprot | Compleasm on Alternate Assembly contigs: Miniprot | n/a |
|
| Compleasm on Alternate Assembly contigs: Translated Proteins | Compleasm on Alternate Assembly contigs: Translated Proteins | n/a |
|
| Compleasm on Alternate Assembly contigs: Full table Busco | Compleasm on Alternate Assembly contigs: Full table Busco | n/a |
|
| Compleasm on Alternate Assembly contigs: Full table | Compleasm on Alternate Assembly contigs: Full table | 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
v0.3.4 (latest) Created 1st Oct 2025 at 03:02 by WorkflowHub Bot
Updated to v0.3.4
Frozen
v0.3.46a322a3
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: 19048 Downloads: 32426 Runs: 17
Created: 20th Oct 2023 at 03:01
Last updated: 1st Oct 2025 at 03:02
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