Assembly-Hifi-HiC-phasing-VGP4/main
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Tests 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
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 | GenomeScope summary generated by K-mer profiling workflow |
|
| HiC forward reads | HiC forward reads | Forward reads as a single dataset in fastq format |
|
| HiC reverse reads | HiC reverse reads | Reverse reads as a single dataset in fastq format |
|
| 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 |
|
| Name for Haplotype 1 | Name for Haplotype 1 | n/a |
|
| Name for Haplotype 2 | Name for Haplotype 2 | n/a |
|
| Pacbio Reads Collection | Pacbio Reads Collection | A simple list containing PacBio data in either fasta or fastq formats. |
|
| SAK input file | SAK input file | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 13 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 |
| 14 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 15 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 16 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 17 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 18 | Cut | Cut1 |
| 19 | Convert | Convert characters1 |
| 20 | Estimated homozygous read coverage | param_value_from_file |
| 21 | Cut | Cut1 |
| 22 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 23 | Estimated genome size | param_value_from_file |
| 24 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0 |
| 25 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 26 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 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 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 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 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 35 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 36 | Data Prep Hap2 | n/a |
| 37 | Data Prep Hap1 | n/a |
| 38 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 39 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 40 | Join two Datasets | join1 |
| 41 | Plot Data | n/a |
| 42 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 43 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 44 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 45 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 |
| 46 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 47 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 48 | merqury_qv | __EXTRACT_DATASET__ |
| 49 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 50 | merqury_stats | __EXTRACT_DATASET__ |
| 51 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 52 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cutadapt on input dataset(s): Read 1 Output | Cutadapt on input dataset(s): Read 1 Output | n/a |
|
| Estimated Genome size | Estimated Genome size | n/a |
|
| raw unitig graph image | raw unitig graph image | n/a |
|
| usable hap2 gfa | usable hap2 gfa | n/a |
|
| usable hap1 gfa | usable hap1 gfa | n/a |
|
| Hifiasm HiC hap2 | Hifiasm HiC hap2 | n/a |
|
| Hifiasm HiC hap1 | Hifiasm HiC hap1 | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Busco Gff File - Hap2 | Busco Gff File - Hap2 | n/a |
|
| Busco Summary Hap2 | Busco Summary Hap2 | n/a |
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| Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
|
| Merqury Stats | Merqury Stats | n/a |
|
| Merqury images | Merqury images | n/a |
|
| Merqury Histograms | Merqury Histograms | n/a |
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| Merqury QV | Merqury QV | n/a |
|
| Busco Summary Hap1 | Busco Summary Hap1 | n/a |
|
| Busco Gff File - Hap1 | Busco Gff File - Hap1 | n/a |
|
| Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
|
| Assembly statistics for Hap1 and Hap2 | Assembly statistics for Hap1 and Hap2 | 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 |
|
| merqury_qv | merqury_qv | n/a |
|
| output_merqury.assembly_01.spectra-cn.fl | output_merqury.assembly_01.spectra-cn.fl | n/a |
|
| merqury_stats | merqury_stats | n/a |
|
| output_merqury.assembly_02.spectra-cn.fl | output_merqury.assembly_02.spectra-cn.fl | n/a |
|
| clean_stats | clean_stats | n/a |
|
Version History
v0.2.2 (latest) Created 13th Aug 2024 at 03:02 by WorkflowHub Bot
Updated to v0.2.2
Frozen
v0.2.2d7114a9
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
ac570c9
Creators and SubmitterActivity
Views: 4110 Downloads: 959 Runs: 0
Created: 4th Nov 2023 at 03:01
AttributionsNone
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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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