Workflow Type: Galaxy
Frozen
Frozen
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
Steps
ID | Name | Description |
---|---|---|
10 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 |
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/0.2.0 |
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/0.19.9+galaxy0 |
23 | Raw Unitig Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
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 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
32 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
33 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
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 Primary | n/a |
37 | Data Prep Alternate | n/a |
38 | merqury_qv | __EXTRACT_DATASET__ |
39 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
40 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
41 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
42 | merqury_stats | __EXTRACT_DATASET__ |
43 | Join two Datasets | join1 |
44 | Plotting Nx and Sizes | n/a |
45 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 |
46 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
Version History
v0.2.1 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot
Updated to v0.2.1
Frozen
v0.2.1
1262df6
v0.1 (earliest) Created 20th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
1f63570
Creators and Submitter
Creators
Not specifiedAdditional credit
Galaxy, VGP
Submitter
Activity
Views: 5408 Downloads: 1343 Runs: 1
Created: 20th Oct 2023 at 03:01
Last updated: 17th Aug 2024 at 03:02
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