Workflow Type: Galaxy
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PacBio 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 |
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FASTQ input | FASTQ input | The FASTQ input to hifiasm can be sourced from the "BAM to FASTQ + QC" sub workflow. |
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Steps
ID | Name | Description |
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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 |
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HiFi Adapter Filter on input dataset(s): clean reads | HiFi Adapter Filter on input dataset(s): clean reads | n/a |
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HiFi Adapter Filter on input dataset(s): contaminant statistic | HiFi Adapter Filter on input dataset(s): contaminant statistic | n/a |
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HiFi Adapter Filter on input dataset(s): contaminant blastout | HiFi Adapter Filter on input dataset(s): contaminant blastout | n/a |
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HiFi Adapter Filter on input dataset(s): blocklist | HiFi Adapter Filter on input dataset(s): blocklist | n/a |
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primary bandage info | primary bandage info | n/a |
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converted FASTA | converted FASTA | n/a |
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primary bandage image | primary bandage image | n/a |
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metrics | metrics | n/a |
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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
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master @ c4797d8 Created 20th Sep 2022 at 01:59 by Johan Gustafsson
Add workflow v2
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Version 1 (earliest) Created 26th Oct 2021 at 01:25 by Johan Gustafsson
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Citation
Price, G., & Farquharson, K. (2022). PacBio HiFi genome assembly using hifiasm v2.1. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.221.3
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Views: 7781 Downloads: 594 Runs: 1
Created: 26th Oct 2021 at 01:25
Last updated: 24th Oct 2022 at 02:55
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