Purge-duplicates-one-haplotype-VGP6b/main
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Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 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+galaxy1 |
| 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
v0.7.6 (latest) Created 2nd May 2025 at 03:02 by WorkflowHub Bot
Updated to v0.7.6
Frozen
v0.7.602d8ffd
v0.1 (earliest) Created 15th Feb 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
49773bd
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Views: 6294 Downloads: 1943 Runs: 1
Created: 15th Feb 2024 at 03:01
Last updated: 2nd May 2025 at 03:02
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