Workflow Type: Galaxy
Stable

BAM-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
  • File

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
  • File
BAM file information BAM file information n/a
  • File
FastQC HTML FastQC HTML n/a
  • File
FastQC text file FastQC text file n/a
  • File

Version History

main @ 1d969fc (latest) Created 17th Oct 2022 at 03:51 by Johan Gustafsson

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Price, G. (2022). BAM to FASTQ + QC v1.0. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.220.2
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Created: 21st Oct 2021 at 06:52

Last updated: 17th Oct 2022 at 03:51

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