Partial ref-guided workflow - gstacks and pops v1.0
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These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.
Galaxy Australia: https://usegalaxy.org.au/
Stacks: http://catchenlab.life.illinois.edu/stacks/
This workflow is part of the reference-guided stacks workflow, https://workflowhub.eu/workflows/347
This workflow takes in bam files and a population map.
To generate bam files see: https://workflowhub.eu/workflows/351
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bam files | Bam files | n/a |
|
| Population map | Population map | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Stacks2: gstacks | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy2 |
| 3 | Stacks2: populations | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites | Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites | n/a |
|
| Stacks2: gstacks on input dataset(s) log file | Stacks2: gstacks on input dataset(s) log file | n/a |
|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| Stacks2: populations on input dataset(s) Summary of Population-level summary statistics | Stacks2: populations on input dataset(s) Summary of Population-level summary statistics | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| Stacks2: populations on input dataset(s) log file | Stacks2: populations on input dataset(s) log file | n/a |
|
| Stacks2: populations on input dataset(s) Population-level haplotype summary statistics | Stacks2: populations on input dataset(s) Population-level haplotype summary statistics | n/a |
|
| Stacks2: populations on input dataset(s) Populations log distributions | Stacks2: populations on input dataset(s) Populations log distributions | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| Stacks2: populations on input dataset(s) Population-level summary statistics | Stacks2: populations on input dataset(s) Population-level summary statistics | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| Haplotypes | Stacks2: populations on input dataset(s) Raw Genotypes/Haplotypes | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
Version History
v1.0
Views: 6565 Downloads: 595 Runs: 0
Created: 31st May 2022 at 09:12
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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
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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.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
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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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