BatchConvert

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). Therefore, input and output locations can be specified as local ...

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) ...