Assembly-Hifi-Trio-phasing-VGP5/main
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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
Steps
| ID | Name | Description |
|---|---|---|
| 16 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 |
| 17 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 18 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 19 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 20 | Cut | Cut1 |
| 21 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 22 | Parse parameter value | param_value_from_file |
| 23 | Convert | Convert characters1 |
| 24 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 25 | Cut | Cut1 |
| 26 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0 |
| 27 | Estimated genome size | param_value_from_file |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 29 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 30 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 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 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 37 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 38 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 39 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 40 | Data prep Hap1 | n/a |
| 41 | Data Prep Hap2 | n/a |
| 42 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 43 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 44 | merqury_qv | __EXTRACT_DATASET__ |
| 45 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 46 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 47 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 48 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 49 | merqury_stats | __EXTRACT_DATASET__ |
| 50 | Plots | n/a |
| 51 | Join two Datasets | join1 |
| 52 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 |
| 53 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
Version History
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.121959c8
Creators and SubmitterActivity
Views: 3594 Downloads: 748 Runs: 0
Created: 4th Nov 2023 at 03:01
Last updated: 17th Aug 2024 at 03:02
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core, iwc
Organizations: Bots, European Galaxy Team
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