BAM to FASTQ + QC v1.0
View on GitHub
Download RO-Crate
Run on GalaxyBAM-to-FASTQ-QC
General recommendations for using BAM-to-FASTQ-QC
Please see the Genome assembly with hifiasm on Galaxy Australia guide.
Acknowledgements
The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input BAM | Input BAM | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | SamToFastq | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2 |
| 2 | Samtools flagstat | toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3 |
| 3 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Converted FastQ reads | Converted FastQ reads | n/a |
|
| BAM file information | BAM file information | n/a |
|
| FastQC HTML | FastQC HTML | n/a |
|
| FastQC text file | FastQC text file | n/a |
|
Version History
main @ 1d969fc (latest) Created 17th Oct 2022 at 03:51 by Johan Gustafsson
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Created: 21st Oct 2021 at 06:52
Last updated: 17th Oct 2022 at 03:51
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Teams: QCIF Bioinformatics, Galaxy Australia
Organizations: QCIF
https://orcid.org/0000-0003-2439-8650
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
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.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy ...
Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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.
**This WorkflowHub collection ...
