Workflow Type: Galaxy
Frozen
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
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. |
|
Genomescope Model Parameters | Genomescope Model Parameters | GenomeScope model parameters generated by K-mer profiling workflow |
|
Genomescope Summary | Genomescope Summary | n/a |
|
Hapmer Database : Maternal | Hapmer Database : Maternal | n/a |
|
Hapmer Database : Paternal | Hapmer Database : Paternal | 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 |
|
Maternal Illumina reads (hap2) | Maternal Illumina reads (hap2) | n/a |
|
Meryl Database : Child | Meryl Database : Child | n/a |
|
Name for Haplotype 1 | Name for Haplotype 1 | n/a |
|
Name for Haplotype 2 | Name for Haplotype 2 | n/a |
|
Pacbio Reads Collection : child | Pacbio Reads Collection : child | n/a |
|
Paternal Illumina reads (hap1) | Paternal Illumina reads (hap1) | n/a |
|
SAK input file (Optional) | SAK input file (Optional) | n/a |
|
Utilize homology information to correct trio-phasing errors | Utilize homology information to correct trio-phasing errors | --trio-dual option |
|
Steps
ID | Name | Description |
---|---|---|
15 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0 |
16 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
17 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
18 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
19 | Cut | Cut1 |
20 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
21 | Parse parameter value | param_value_from_file |
22 | Convert | Convert characters1 |
23 | Homozygous read coverage for Hifiasm | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
24 | Cut | Cut1 |
25 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0 |
26 | Estimated genome size | param_value_from_file |
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 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
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 | 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 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
37 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
38 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
39 | Data prep Hap1 | n/a |
40 | Data Prep Hap2 | n/a |
41 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
42 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
43 | Plots | n/a |
44 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
json_stats | json_stats | n/a |
|
multiqc html report | multiqc html report | n/a |
|
cutadapt multiqc stats | cutadapt multiqc stats | n/a |
|
Estimated Genome size | Estimated Genome size | n/a |
|
usable hap1 gfa | usable hap1 gfa | n/a |
|
usable hap2 gfa | usable hap2 gfa | n/a |
|
Hifiasm Trio hap1 | Hifiasm Trio hap1 | n/a |
|
Hifiasm Trio hap2 | Hifiasm Trio hap2 | n/a |
|
Busco Gff Hap1 | Busco Gff Hap1 | n/a |
|
Busco Summary Hap1 | Busco Summary Hap1 | n/a |
|
Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
|
Busco Gff Hap2 | Busco Gff Hap2 | n/a |
|
Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
|
Busco Summary Hap2 | Busco Summary Hap2 | n/a |
|
Merqury Images | Merqury Images | n/a |
|
Merqury Trio Histogram | Merqury Trio Histogram | n/a |
|
Size Plot | Size Plot | n/a |
|
Nx Plot | Nx Plot | n/a |
|
Assembly statistics for Hap1 and Hap2 | Assembly statistics for Hap1 and Hap2 | n/a |
|
Version History
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
21959c8
Creators and Submitter
Creators
Not specifiedAdditional credit
Galaxy, VGP
Submitter
Activity
Views: 4539 Downloads: 1002 Runs: 0
Created: 4th Nov 2023 at 03:01
Last updated: 17th Aug 2024 at 03:02
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