Assembly-Hifi-only-VGP3/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
- Haplotype 2 assembly
- 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 assemblie
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bits for Hifiasm bloom filter | Bits for Hifiasm 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 |
|
| 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 | n/a |
|
| Name of alternate assembly | Name of alternate assembly | n/a |
|
| Name of primary assembly | Name of primary assembly | n/a |
|
| Pacbio Reads Collection | Pacbio Reads Collection | n/a |
|
| SAK input file (Optional) | SAK input file (Optional) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0 |
| 11 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 12 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.1.0 |
| 13 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 14 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 15 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 16 | Cut | Cut1 |
| 17 | Convert | Convert characters1 |
| 18 | Parse parameter value | param_value_from_file |
| 19 | Cut | Cut1 |
| 20 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 21 | Estimated genome size | param_value_from_file |
| 22 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1 |
| 23 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 24 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 25 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 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 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 32 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 33 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 34 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 35 | Data Prep Primary | n/a |
| 36 | Data Prep Alternate | n/a |
| 37 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
| 38 | Plotting Nx and Sizes | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| multiqc html report | multiqc html report | n/a |
|
| cutadapt multiqc stats | cutadapt multiqc stats | n/a |
|
| Estimated Genome size | Estimated Genome size | n/a |
|
| Hifiasm Alternate gfa | Hifiasm Alternate gfa | n/a |
|
| Hifiasm Primary gfa | Hifiasm Primary gfa | n/a |
|
| Usable GFA Alternate | Usable GFA Alternate | n/a |
|
| Usable GFA Primary | Usable GFA Primary | n/a |
|
| Hifiasm Primary assembly | Hifiasm Primary assembly | n/a |
|
| Hifiasm Alternate assembly | Hifiasm Alternate assembly | n/a |
|
| Assembly Stats on Primary assembly | Assembly Stats on Primary assembly | n/a |
|
| Assembly Stats on Alternate Assembly | Assembly Stats on Alternate Assembly | n/a |
|
| Busco summary image | Busco summary image | n/a |
|
| Merqury png | Merqury png | n/a |
|
| Merqury Histograms | Merqury Histograms | n/a |
|
| Merqury completeness stats | Merqury completeness stats | n/a |
|
| Assembly statistics | Assembly statistics | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
Version History
v0.2.1 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot
Updated to v0.2.1
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v0.2.11262df6
v0.1 (earliest) Created 20th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
1f63570
Creators and Submitter
Activity
Views: 5452 Downloads: 1364 Runs: 1
Created: 20th Oct 2023 at 03:01
Last updated: 17th Aug 2024 at 03:02
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