BAM to FASTQ + QC v1.0
main @ 1d969fc (latest)

main @ 1d969fc (latest)

Version 1 (earliest)

View on GitHub

Download RO-Crate

Run on Galaxy

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).

SEEK ID: https://workflowhub.eu/workflows/220?version=2

DOI: 10.48546/workflowhub.workflow.220.2

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