HPRC Release 2

Repo Organization

Data Tables

If you are looking for how to get the assemblies or information about the assemblies, navigate to the data_tables folder.

Uploading Results

How to upload Release 2 analysis outputs

• Reach out on the #Data channel of the HPRC Slack to request credentials for the HPRC bucket
• Organize your data by sample and name with the assembly name.
  • Organize the files by sample to allow for easier indexing
    • For example upload_folder/{sample_id}/sniffles/
  • The assembly name can be found in the assembly index and should be used as a "key" to ensure that users know which file was used to create the results.
    • For example, analysis done for assembly HG00408_pat_hprc_r2_v1.0.1 should be named HG00408_pat_hprc_r2_v1.0.1.yourtool.bed
• Follow the instructions to upload data to the bucket

Criteria for upload & indexing of results

Analysis results should be uploaded to the S3 bucket if they are reasonably expected to be useful across the consortium.

Notes

The following folders are used for tracking and aiding assembly and assembly QC production.

• assembly: assembly notes and tracking
• polishing: polishing of raw assemblies
• upload: clean up and upload to Genbank (including contamination fixes)
• download: download and renaming of assemblies from Genbank
• assembly_qc: QC of genbank assemblies
• hpc: helper scripts for launching analysis
• reference_data: notes on reference data provenance