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 ([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. |
|
Genomescope Model Parameters | Genomescope Model Parameters | n/a |
|
Genomescope Summary | Genomescope Summary | n/a |
|
HiC forward reads | HiC forward reads | n/a |
|
HiC reverse reads | HiC reverse reads | n/a |
|
Lineage | Lineage | n/a |
|
Meryl Database | Meryl Database | 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 | Pacbio Reads Collection | n/a |
|
SAK input file | SAK input file | n/a |
|
Steps
ID | Name | Description |
---|---|---|
11 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 |
12 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
13 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
14 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
15 | Cut | Cut1 |
16 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
17 | Estimated homozygous read coverage | param_value_from_file |
18 | Convert | Convert characters1 |
19 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4 |
20 | Cut | Cut1 |
21 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
22 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
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 | 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 | Estimated genome size | param_value_from_file |
29 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
30 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
31 | gfastats_data_prep | n/a |
32 | gfastats_data_prep | n/a |
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 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
36 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
37 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
38 | gfastats_plot | n/a |
39 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
40 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
41 | Cut | Cut1 |
42 | Paste | Paste1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Cutadapt on input dataset(s): Read 1 Output | Cutadapt on input dataset(s): Read 1 Output | n/a |
|
usable hap1 gfa | usable hap1 gfa | n/a |
|
usable hap2 gfa | usable hap2 gfa | n/a |
|
Estimated Genome size | Estimated Genome size | n/a |
|
Hifiasm HiC hap1 | Hifiasm HiC hap1 | n/a |
|
Hifiasm HiC hap2 | Hifiasm HiC hap2 | n/a |
|
Busco Summary Hap1 | Busco Summary Hap1 | n/a |
|
Busco Summary Image Hap1 | Busco Summary Image Hap1 | n/a |
|
Merqury images | Merqury images | n/a |
|
Busco Summary Image Hap2 | Busco Summary Image Hap2 | n/a |
|
Busco Summary Hap2 | Busco Summary Hap2 | n/a |
|
Nx Plot | Nx Plot | n/a |
|
Size Plot | Size Plot | n/a |
|
Assembly statistics fir Hap1 and Hap2 | Assembly statistics fir Hap1 and Hap2 | n/a |
|
Version History
v0.1.3 (latest) Created 3rd Oct 2024 at 03:05 by WorkflowHub Bot
Updated to v0.1.3
Frozen
v0.1.3
e076662
v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
ac570c9
Creators and Submitter
Creator
Additional credit
Galaxy, VGP
Submitter
Activity
Views: 4663 Downloads: 1102 Runs: 0
Created: 4th Nov 2023 at 03:01
Attributions
None