Partial de novo workflow: c-s-g-pops only Version 1
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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 takes in ustacks output, and runs cstacks, sstacks and gstacks.
To generate ustacks output see https://workflowhub.eu/workflows/349
For the full de novo workflow see https://workflowhub.eu/workflows/348
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Population map | Population map | n/a |
|
| Ustacks inputs | Ustacks inputs | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Stacks2: cstacks | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy2 |
| 3 | Stacks2: sstacks | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/2.55+galaxy2 |
| 4 | Stacks2: tsv2bam | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/2.55+galaxy2 |
| 5 | Stacks2: gstacks | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy2 |
| 6 | Stacks2: populations | toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Stacks2: cstacks on input dataset(s) Catalog of loci | Stacks2: cstacks on input dataset(s) Catalog of loci | n/a |
|
| Stacks2: cstacks on input dataset(s) log file | Stacks2: cstacks on input dataset(s) log file | n/a |
|
| Stacks2: sstacks on input dataset(s) log file | Stacks2: sstacks on input dataset(s) log file | n/a |
|
| Stacks2: sstacks on input dataset(s) Matches to the catalog | Stacks2: sstacks on input dataset(s) Matches to the catalog | n/a |
|
| Stacks2: tsv2bam on input dataset(s) log file | Stacks2: tsv2bam on input dataset(s) log file | n/a |
|
| Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) | Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) | n/a |
|
| 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_2 | _anonymous_output_2 | n/a |
|
| Stacks2: populations on input dataset(s) Populations log distributions | Stacks2: populations on input dataset(s) Populations log distributions | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | 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 |
|
| Stacks2: populations on input dataset(s) log file | Stacks2: populations on input dataset(s) log file | n/a |
|
| Haplotypes | Stacks2: populations on input dataset(s) Raw Genotypes/Haplotypes | 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_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | 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 |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
Version History
v1.0
Views: 2373
Created: 31st May 2022 at 08:56
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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
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
Public web page: https://www.biocommons.org.au/
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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