Workflow Type: Galaxy
Frozen
Stable
Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.
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 |
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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 |
|
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 (earliest) Created 21st Mar 2023 at 04:30 by Johan Gustafsson
Add workflow v2.1
Frozen
v2.1.0
499acb1
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
Submitter
Citation
Price, G., & Farquharson, K. (2022). {PacBio-HiFi-genome-assembly-using-hifiasm}. https://doi.org/["DOI goes here"]
License
Activity
Views: 721 Downloads: 167
Created: 21st Mar 2023 at 04:30
Annotated Properties
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
None