Assembly-Hifi-HiC-phasing-VGP4/main
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Workflow Type: Galaxy
Frozen
Assemble Genome using PacBio HiFi and HiC data from the same individual for phasing. Prerequisite: Run k-mer profiling workflow (VGP1). This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury histograms, 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 | Select the database to use for Busco lineages. |
|
| Genomescope Model Parameters | Genomescope Model Parameters | GenomeScope model parameters generated by K-mer profiling workflow |
|
| Genomescope Summary | Genomescope Summary | GenomeScope summary generated by K-mer profiling workflow |
|
| Hi-C reads - Forward | Hi-C reads - Forward | n/a |
|
| Hi-C reads - Reverse | Hi-C reads - Reverse | n/a |
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| 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 | Meryl database generated by K-mer profiling workflow |
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| Name for Haplotype 1 | Name for Haplotype 1 | Name of the first haplotype without blank space. |
|
| Name for Haplotype 2 | Name for Haplotype 2 | Name of the second haplotype without blank space. |
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| Pacbio Reads | Pacbio Reads | A simple list containing PacBio data in either fasta or fastq formats. |
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| SAK input file | SAK input file | Do not use. |
|
| Trim Hi-C reads? | Trim Hi-C reads? | Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy". |
|
Steps
| ID | Name | Description |
|---|---|---|
| 14 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 15 | Sort Forward | __SORTLIST__ |
| 16 | Sort Reverse | __SORTLIST__ |
| 17 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0 |
| 18 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 19 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 20 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 21 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 22 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0 |
| 23 | Cut | Cut1 |
| 24 | Pick forward | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 25 | Pick reverse | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 26 | Convert | Convert characters1 |
| 27 | Estimated homozygous read coverage | param_value_from_file |
| 28 | Collapse forward reads | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 29 | Collapse reverse reads | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 30 | Cut | Cut1 |
| 31 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 32 | Estimated genome size | param_value_from_file |
| 33 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
| 34 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 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 gfa hap2 no sequences | 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 | gfastats gfa hap1 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 41 | gfastats gfa hap2 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 42 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 43 | gfastats gfa hap1 no sequences | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 44 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0 |
| 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 | Data Prep Hap2 | n/a |
| 48 | Data Prep Hap1 | n/a |
| 49 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0 |
| 50 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0 |
| 51 | Join two Datasets | join1 |
| 52 | Plot Data | n/a |
| 53 | Busco Hap2 | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 54 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 55 | Busco Hap1 | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 56 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0 |
| 57 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 58 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 59 | merqury_qv | __EXTRACT_DATASET__ |
| 60 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 61 | merqury_stats | __EXTRACT_DATASET__ |
| 62 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 63 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cutadapt on input dataset(s): Read 1 Output | Cutadapt on input dataset(s): Read 1 Output | n/a |
|
| Clean Hi-C forward reads | Clean Hi-C forward reads | n/a |
|
| Clean Hi-C reverse reads | Clean Hi-C reverse reads | n/a |
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| Estimated Genome size | Estimated Genome size | n/a |
|
| raw unitig graph image | raw unitig graph image | n/a |
|
| No Sequences hap2 gfa | No Sequences hap2 gfa | n/a |
|
| usable hap1 gfa | usable hap1 gfa | n/a |
|
| usable hap2 gfa | usable hap2 gfa | n/a |
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| No sequences hap1 gfa | No sequences hap1 gfa | n/a |
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| Hifiasm Hi-C hap2 | Hifiasm Hi-C hap2 | n/a |
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| Hifiasm Hi-C hap1 | Hifiasm Hi-C hap1 | n/a |
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| Size Plot | Size Plot | n/a |
|
| Nx Plot | Nx Plot | n/a |
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| Busco Summary Hap2 | Busco Summary Hap2 | n/a |
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| Busco Gff File - Hap2 | Busco Gff File - Hap2 | n/a |
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| Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
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| Merqury Histograms | Merqury Histograms | n/a |
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| Merqury QV | Merqury QV | n/a |
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| Merqury Stats | Merqury Stats | n/a |
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| Merqury images | Merqury images | n/a |
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| Busco Gff File - Hap1 | Busco Gff File - Hap1 | n/a |
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| Busco Summary Hap1 | Busco Summary Hap1 | n/a |
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| Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
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| Assembly statistics for Hap1 and Hap2 | Assembly statistics for Hap1 and Hap2 | n/a |
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| output_merqury.spectra-cn.fl | output_merqury.spectra-cn.fl | n/a |
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| output_merqury.spectra-asm.fl | output_merqury.spectra-asm.fl | n/a |
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| merqury_qv | merqury_qv | n/a |
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| output_merqury.assembly_01.spectra-cn.fl | output_merqury.assembly_01.spectra-cn.fl | n/a |
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| merqury_stats | merqury_stats | n/a |
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| output_merqury.assembly_02.spectra-cn.fl | output_merqury.assembly_02.spectra-cn.fl | n/a |
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| clean_stats | clean_stats | n/a |
|
Version History
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1ac570c9
Creators and Submitter
Activity
Views: 18694 Downloads: 30253 Runs: 0
Created: 4th Nov 2023 at 03:01
Last updated: 26th Mar 2025 at 10:06
AttributionsNone
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