PacBio HiFi genome assembly using hifiasm v2.1
View on GitHub
Download RO-Crate
Run on GalaxyAssembly, 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
Frozen
v2.1.0499acb1
master @ c4797d8 Created 20th Sep 2022 at 01:59 by Johan Gustafsson
Add workflow v2
Frozen
masterc4797d8
Version 1 (earliest) Created 26th Oct 2021 at 01:25 by Johan Gustafsson
Frozen
Version-1
9df3cb5
Creators and Submitter
Views: 15828 Downloads: 1979 Runs: 9
Created: 26th Oct 2021 at 01:25
Last updated: 24th Oct 2022 at 02:55
Tags AttributionsNone
Collections
HiFi genome assembl...
Related items
Teams: QCIF Bioinformatics, Galaxy Australia
Organizations: QCIF
https://orcid.org/0000-0003-2439-8650
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia, National Computational Infrastructure (NCI) WorkflowHub team
Web page: https://www.biocommons.org.au/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy ...
Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
This ARDC and BioCommons sponsored project delivers a key component of BioCommon’s vision for an ecosystem of platforms providing researchers with sophisticated data analysis and digital asset stewardship capabilities. The Bring Your Own Data (BYOD) Platform (https://www.biocommons.org.au/byod-expansion) has enabled highly accessible, highly available, highly scalable analysis and data sharing capabilities for the benefit of life science researchers nationally.
**This WorkflowHub collection ...
