Genome Assembly using PacBio data 1.0
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Run on GalaxyGenome Assembly using PacBio data and Flye or Hifiasm assembler
Associated Tutorial
This workflows is part of the tutorial Genome assembly using PacBio data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier, Solenne Correard
Tutorial Author(s): Anthony Bretaudeau, Alexandre Cormier, Erwan Corre, Laura Leroi, Stéphanie Robin, Solenne Correard
Tutorial Contributor(s): Helena Rasche, Anthony Bretaudeau, Stéphanie Robin, Cristóbal Gallardo, Saskia Hiltemann, Björn Grüning, Solenne Correard, Bérénice Batut
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| PacBio reads | #main/PacBio reads | PacBio reads in fastq format |
|
| Reference genome | #main/Reference genome | Reference genome from JGI |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Flye | toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0 |
| 3 | Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
| 4 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
| 5 | Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
| 6 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3 |
| 7 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Flye on input dataset(s): assembly graph | #main/Flye on input dataset(s): assembly graph | n/a |
|
| Flye on input dataset(s): assembly info | #main/Flye on input dataset(s): assembly info | n/a |
|
| Flye on input dataset(s): consensus | #main/Flye on input dataset(s): consensus | n/a |
|
| Flye on input dataset(s): graphical fragment assembly | #main/Flye on input dataset(s): graphical fragment assembly | n/a |
|
| Quast on input dataset(s): HTML report | #main/Quast on input dataset(s): HTML report | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
Version History
master
Creators and Submitter
Views: 1256 Downloads: 178 Runs: 4
Created: 2nd Jun 2025 at 11:01
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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