Assembly-Hifi-Trio-phasing-VGP5/main
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Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bits for bloom filter | Bits for 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 |
|
| Hapmer Database : Maternal | Hapmer Database : Maternal | n/a |
|
| Hapmer Database : Paternal | Hapmer Database : Paternal | 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 |
|
| Maternal Illumina reads (hap2) | Maternal Illumina reads (hap2) | n/a |
|
| Meryl Database : Child | Meryl Database : Child | n/a |
|
| Name for Haplotype 1 | Name for Haplotype 1 | n/a |
|
| Name for Haplotype 2 | Name for Haplotype 2 | n/a |
|
| Pacbio Reads Collection : child | Pacbio Reads Collection : child | n/a |
|
| Paternal Illumina reads (hap1) | Paternal Illumina reads (hap1) | n/a |
|
| Utilize homology information to correct trio-phasing errors | Utilize homology information to correct trio-phasing errors | --trio-dual option |
|
Steps
| ID | Name | Description |
|---|---|---|
| 15 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 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 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0 |
| 19 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 20 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 21 | Cut | Cut1 |
| 22 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0 |
| 23 | Parse parameter value | param_value_from_file |
| 24 | Convert | Convert characters1 |
| 25 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 26 | Cut | Cut1 |
| 27 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
| 28 | Estimated genome size | param_value_from_file |
| 29 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 30 | No Sequence hap2 gfa | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 31 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 32 | No Sequence hap1 gfa | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 33 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 34 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 36 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 37 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 38 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 39 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 40 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 41 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 42 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 43 | Data prep Hap1 | n/a |
| 44 | Data Prep Hap2 | n/a |
| 45 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 46 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 47 | merqury_qv | __EXTRACT_DATASET__ |
| 48 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 49 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 50 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 51 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 52 | merqury_stats | __EXTRACT_DATASET__ |
| 53 | Plots | n/a |
| 54 | Join two Datasets | join1 |
| 55 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0 |
| 56 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| json_stats | json_stats | 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 |
|
| usable hap1 gfa | usable hap1 gfa | n/a |
|
| No Sequence hap2 gfa | No Sequence hap2 gfa | n/a |
|
| raw unitig graph image | raw unitig graph image | n/a |
|
| No Sequence hap1 gfa | No Sequence hap1 gfa | n/a |
|
| usable hap2 gfa | usable hap2 gfa | n/a |
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| Hifiasm Trio hap1 | Hifiasm Trio hap1 | n/a |
|
| Hifiasm Trio hap2 | Hifiasm Trio hap2 | n/a |
|
| Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
|
| Busco Summary Hap1 | Busco Summary Hap1 | n/a |
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| Busco Gff Hap1 | Busco Gff Hap1 | n/a |
|
| Busco Summary Hap2 | Busco Summary Hap2 | n/a |
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| Busco Gff Hap2 | Busco Gff Hap2 | n/a |
|
| Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
|
| Merqury Images | Merqury Images | n/a |
|
| Merqury QV | Merqury QV | n/a |
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| Merqury Trio Histogram | Merqury Trio Histogram | 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 |
|
| output_merqury.assembly_02.spectra-cn.fl | output_merqury.assembly_02.spectra-cn.fl | n/a |
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| merqury_stats | merqury_stats | n/a |
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| Nx Plot | Nx Plot | n/a |
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| Size Plot | Size Plot | n/a |
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| Assembly statistics for Hap1 and Hap2 | Assembly statistics for Hap1 and Hap2 | n/a |
|
| clean_stats | clean_stats | n/a |
|
Version History
v0.9.3 (latest) Created 2nd May 2025 at 03:02 by WorkflowHub Bot
Updated to v0.9.3
Frozen
v0.9.3c76df93
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
21959c8
Creators and Submitter
Activity
Views: 9250 Downloads: 2625 Runs: 1
Created: 4th Nov 2023 at 03:01
Last updated: 2nd May 2025 at 03:02
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