Workflow Type: Galaxy
Frozen
Frozen
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Stable
Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.
Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)
Inputs
ID | Name | Description | Type |
---|---|---|---|
FASTQ input | FASTQ input | The FASTQ input to hifiasm can be sourced from the "BAM to FASTQ + QC" sub workflow. |
|
Steps
ID | Name | Description |
---|---|---|
1 | hifiasm assembly | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.15.4+galaxy0 |
2 | Haplotype resolved Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
3 | Haplotype resolved Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
4 | Processed unitig Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
5 | Processed unitig Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
6 | Alternate assembly Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
7 | Primary assembly Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
8 | Convert primary assembly GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
9 | Primary assembly Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
10 | Alternate assembly Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
11 | Primary assembly Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
primary bandage info | primary bandage info | n/a |
|
converted FASTA | converted FASTA | n/a |
|
primary bandage image | primary bandage image | n/a |
|
metrics | metrics | n/a |
|
Version History
v2.1.0 (latest) Created 21st Oct 2022 at 06:13 by Johan Gustafsson
Add workflow v2.1
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v2.1.0
499acb1
master @ c4797d8 Created 20th Sep 2022 at 01:59 by Johan Gustafsson
Add workflow v2
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master
c4797d8
Version 1 (earliest) Created 26th Oct 2021 at 01:25 by Johan Gustafsson
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Version-1
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Views: 7786 Downloads: 594 Runs: 1
Created: 26th Oct 2021 at 01:25
Last updated: 24th Oct 2022 at 02:55
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