auto_process_ngs
0.67

Getting started

  • Overview
  • Requirements
  • Installation
  • Configuration

Pipeline stages

  • Starting an analysis
  • Fastq generation
  • Setting up projects
  • Running QC
  • Publishing QC
  • Archiving analyses
  • Troubleshooting

Post-processing

  • Reporting analyses
  • Managing and sharing data
  • Importing projects
  • Running QC stand-alone

Single cell data

  • 10x Genomics single cell data
  • Parse Evercode data
  • Bio-Rad ddSEQ single cell data

Spatial data

  • 10x Genomics Visium data

Helpers

  • Sample sheet manipulations

Control files

  • projects.info
  • 10x_multiome_libraries.info
  • 10x_multi_config[.SAMPLE].csv

Outputs

  • Analysis and project directories
  • Processing QC
  • Barcode analysis
  • QC reports

Reference Documentation

  • auto_process commands
  • Utilities
  • QC protocol specification

Developer Documentation

  • Updating CellRanger
  • Developers’ API documentation
auto_process_ngs
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