PacBio HiFi genome assembly using hifiasm v2.1 v2.1.0
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Download RO-CrateAssembly, 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 |
|
| 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 (earliest) Created 21st Mar 2023 at 02:48 by Johan Gustafsson
Add workflow v2.1
Frozen
v2.1.0499acb1
Creators and SubmitterViews: 930 Downloads: 250
Created: 21st Mar 2023 at 02:48
Tags AttributionsNone
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