Purge-duplicates-one-haplotype-VGP6b/main
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Workflow Type: Galaxy
Frozen
Frozen
Tests Purge duplicates from one haplotype. Prerequisites: run after a k-mer profiling workflow (VGP 1 or 2) and a contiging workflow (VGP 3,4 or 5).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly to leave alone (For Merqury comparison) | Assembly to leave alone (For Merqury comparison) | Assembly that does not need purging. |
|
| Assembly to purge | Assembly to purge | Assembly containing duplications to be purged. |
|
| Database for Busco Lineage | Database for Busco Lineage | Database to use for Busco lineages. |
|
| Estimated genome size - Parameter File | Estimated genome size - Parameter File | Estimated genome file obtained in the contiging workflow. |
|
| Genomescope model parameters | Genomescope model parameters | Model parameters obtained in the k-mer profiling workflow. |
|
| Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis |
|
| Meryl Database | Meryl Database | Meryl database obtained in the k-mer profiling workflow. |
|
| Name of purged assembly | Name of purged assembly | n/a |
|
| Name of un-altered assembly | Name of un-altered assembly | n/a |
|
| Pacbio Reads Collection - Trimmed | Pacbio Reads Collection - Trimmed | Trimmed PacBio HiFi reads—outputs of cutadapt in the contiging workflow. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 11 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 12 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 13 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 14 | Estimated genome size | param_value_from_file |
| 15 | Cut | Cut1 |
| 16 | Cut | Cut1 |
| 17 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 18 | gfastats_data_prep | n/a |
| 19 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 20 | Parse parameter value | param_value_from_file |
| 21 | Parse parameter value | param_value_from_file |
| 22 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 23 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 24 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 25 | Remove REPEATs from BED | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0 |
| 26 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 27 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 29 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0 |
| 30 | Convert purged fasta to gfa | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 32 | merqury_QV | __EXTRACT_DATASET__ |
| 33 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 34 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 35 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 36 | merqury_stats | __EXTRACT_DATASET__ |
| 37 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 38 | gfastats_data_prep | n/a |
| 39 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 40 | gfastats_plot | n/a |
| 41 | Join two Datasets | join1 |
| 42 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0 |
| 43 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cutoffs | Cutoffs | n/a |
|
| Read Coverage and cutoffs calculation: Histogram plot | Read Coverage and cutoffs calculation: Histogram plot | n/a |
|
| Removed haplotigs | Removed haplotigs | n/a |
|
| Purged assembly | Purged assembly | n/a |
|
| Merqury on Phased assemblies: Images | Merqury on Phased assemblies: Images | n/a |
|
| Merqury on Phased assemblies: stats | Merqury on Phased assemblies: stats | n/a |
|
| qv_files | qv_files | n/a |
|
| Busco on Purged Primary assembly: summary image | Busco on Purged Primary assembly: summary image | n/a |
|
| Busco on Purged Primary assembly: short summary | Busco on Purged Primary assembly: short summary | n/a |
|
| Purged assembly (GFA) | Purged assembly (GFA) | n/a |
|
| Purged assembly statistics | Purged assembly statistics | 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 |
|
| output_merqury.assembly_02.spectra-cn.fl | output_merqury.assembly_02.spectra-cn.fl | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Assembly statistics for both assemblies | Assembly statistics for both assemblies | n/a |
|
| clean_stats | clean_stats | n/a |
|
Version History
v0.8.5 (latest) Created 29th Jan 2026 at 03:01 by WorkflowHub Bot
Updated to v0.8.5
Frozen
v0.8.5a3e0acc
v0.1 (earliest) Created 15th Feb 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
49773bd
Creators and Submitter
Activity
Views: 16590 Downloads: 91710 Runs: 6
Created: 15th Feb 2024 at 03:01
Last updated: 29th Jan 2026 at 03:01
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