Assembly-Hifi-Trio-phasing-VGP5/main
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Tests Assembly with Hifi reads and Trio Data
Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing
Inputs
- Hifi long reads [fastq]
- Concatenated Illumina reads : Paternal [fastq]
- Concatenated Illumina reads : Maternal [fastq]
- K-mer database [meryldb]
- Paternal hapmer database [meryldb]
- Maternal hapmer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Genome model parameters generated by Genomescope [tabular]
- Homozygous read coverage (Estimated from the Genomescope model if not provided)
- Lineage of the species being assembled
- Bloom Filter
- Name of first haplotype
- Name of second haplotype
Outputs
- Haplotype 1 assembly
- Haplotype 2 assembly
- QC: BUSCO report for both assemblies
- Merqury report for both assemblies
- Assembly statistics for both assemblies
- Nx Plot for both assemblies
- Size plot for both assemblies
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. |
|
| 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 |
|
| SAK input file (Optional) | SAK input file (Optional) | 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/4.8+galaxy0 |
| 16 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 17 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 18 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 19 | Cut | Cut1 |
| 20 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
| 21 | Parse parameter value | param_value_from_file |
| 22 | Convert | Convert characters1 |
| 23 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 24 | Cut | Cut1 |
| 25 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1 |
| 26 | Estimated genome size | param_value_from_file |
| 27 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 29 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 30 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 33 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 34 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 36 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 37 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 38 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 39 | Data prep Hap1 | n/a |
| 40 | Data Prep Hap2 | n/a |
| 41 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 42 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 43 | Plots | n/a |
| 44 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+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 |
|
| usable hap2 gfa | usable hap2 gfa | n/a |
|
| Hifiasm Trio hap1 | Hifiasm Trio hap1 | n/a |
|
| Hifiasm Trio hap2 | Hifiasm Trio hap2 | n/a |
|
| Busco Gff Hap1 | Busco Gff Hap1 | n/a |
|
| Busco Summary Hap1 | Busco Summary Hap1 | n/a |
|
| Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
|
| Busco Gff Hap2 | Busco Gff Hap2 | n/a |
|
| Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
|
| Busco Summary Hap2 | Busco Summary Hap2 | n/a |
|
| Merqury Images | Merqury Images | n/a |
|
| Merqury Trio Histogram | Merqury Trio Histogram | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Assembly statistics for Hap1 and Hap2 | Assembly statistics for Hap1 and Hap2 | n/a |
|
Version History
v0.9.9 (latest) Created 1st Oct 2025 at 03:01 by WorkflowHub Bot
Updated to v0.9.9
Frozen
v0.9.9ba1ceb8
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: 24061 Downloads: 150022 Runs: 2
Created: 4th Nov 2023 at 03:01
Last updated: 1st Oct 2025 at 03:01
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Computer Science
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