PacBio HiFi genome assembly using hifiasm v2.1
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Run on GalaxyPacBio HiFi genome assembly using hifiasm v2.1
General usage recommendations
Please see the Genome assembly with hifiasm on Galaxy Australia guide.
See change log
Acknowledgements
The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).
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 | HiFi Adapter Filter | toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/2.0.0+galaxy0 |
| 2 | hifiasm assembly | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy3 |
| 3 | Haplotype resolved Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
| 4 | Haplotype resolved 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 | Processed unitig Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
| 7 | Alternate assembly Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
| 8 | Primary assembly Bandage info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
| 9 | Convert primary assembly GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 10 | Alternate assembly Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
| 11 | Primary assembly Bandage image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3 |
| 12 | Primary assembly Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| HiFi Adapter Filter on input dataset(s): clean reads | HiFi Adapter Filter on input dataset(s): clean reads | n/a |
|
| HiFi Adapter Filter on input dataset(s): contaminant statistic | HiFi Adapter Filter on input dataset(s): contaminant statistic | n/a |
|
| HiFi Adapter Filter on input dataset(s): contaminant blastout | HiFi Adapter Filter on input dataset(s): contaminant blastout | n/a |
|
| HiFi Adapter Filter on input dataset(s): blocklist | HiFi Adapter Filter on input dataset(s): blocklist | n/a |
|
| 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: 8389 Downloads: 690 Runs: 2
Created: 26th Oct 2021 at 01:25
Last updated: 24th Oct 2022 at 02:55
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Teams: QCIF Bioinformatics, Galaxy Australia
Organizations: QCIF
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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/
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/
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.
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Space: Australian BioCommons
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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.
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