Partial ref-guided workflow - bwa mem only 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
Inputs
- demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
- reference genome in fasta format
Outputs
- A set of filtered bam files, ready for the next part of the stacks workflow (e.g. gstacks).
- Statistics on the bam files.
Steps
| ID | Name | Description |
|---|---|---|
| 2 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 3 | Samtools view: filters out unmapped and non-primary mapped reads (see flags) | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 |
| 4 | Samtools stats: BAM stats before filtering | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3 |
| 5 | Samtools stats: BAM stats after filtering | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3 |
| 6 | MultiQC: BAM stats before filtering | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
| 7 | MultiQC: BAM stats after filtering | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
Version History
v1.0
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Created: 31st May 2022 at 09:05
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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.
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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.
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.
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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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