Assembly-Hifi-HiC-phasing-VGP4/main
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Workflow Type: Galaxy
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Contiging Solo w/HiC:
Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.
Inputs
- Hifi long reads [fastq]
- HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
- HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Name of first assembly
- Name of second assembly
Outputs
- Haplotype 1 assembly ([fasta] and [gfa])
- Haplotype 2 assembly ([fasta] and [gfa])
- QC: BUSCO report for both assemblies
- QC: Merqury report for both assemblies
- QC: Assembly statistics for both assemblies
- QC: Nx plot for both assemblies
- QC: Size plot for both assemblies
Steps
| ID | Name | Description |
|---|---|---|
| 14 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 15 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 16 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 17 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 18 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2 |
| 19 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 20 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 21 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 22 | Pick forward 2 | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 23 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2 |
| 24 | Cut | Cut1 |
| 25 | Test if collection has only one item or is empty | n/a |
| 26 | Unzip collection | __UNZIP_COLLECTION__ |
| 27 | Convert | Convert characters1 |
| 28 | Estimated homozygous read coverage | param_value_from_file |
| 29 | Extract Hic forward | __EXTRACT_DATASET__ |
| 30 | Extract Hic reverse | __EXTRACT_DATASET__ |
| 31 | Collapse forward reads | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 32 | Collapse reverse reads | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 33 | Cut | Cut1 |
| 34 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 35 | Hi-C forward reads | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 36 | Hi-C reverse reads | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 37 | Estimated genome size | param_value_from_file |
| 38 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
| 39 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 40 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 41 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 42 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 43 | gfastats gfa hap2 no sequences | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 44 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 45 | gfastats gfa hap1 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 46 | gfastats gfa hap2 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 47 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 48 | gfastats gfa hap1 no sequences | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 49 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 50 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 51 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 52 | Data Prep Hap2 | n/a |
| 53 | Data Prep Hap1 | n/a |
| 54 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2 |
| 55 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2 |
| 56 | Join two Datasets | join1 |
| 57 | Plot Data | n/a |
| 58 | Compleasm Hap2 | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 59 | Compleasm Hap1 | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 60 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 61 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2 |
| 62 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0 |
| 63 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 64 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 65 | merqury_qv | __EXTRACT_DATASET__ |
| 66 | merqury_stats | __EXTRACT_DATASET__ |
| 67 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 68 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 69 | Unique lines | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.5+galaxy2 |
| 70 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0 |
| 71 | Select first | Show beginning1 |
| 72 | Select first | Show beginning1 |
| 73 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0 |
| 74 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 |
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: 24266 Downloads: 125168 Runs: 0
Created: 4th Nov 2023 at 03:01
Last updated: 26th Mar 2025 at 10:06
AttributionsNone
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