auto_process_ngs provides a set of utilities which automate the processing of sequencing data from Illumina Next Generation Sequencing (NGS) platforms, specifically:
- Generation of Fastq files from raw Bcl data produced by the sequencer
- Dividing Fastqs into projects for subsequent analysis
- Running quality checks (QC) on each project
- Copying final data to an archive location ready for appropriate bioinformatic analyses
In addition to standard Illumina sequencing data it can also handle data prepared using a number of single-cell (SC) RNA-seq platforms.
Together these utilities form the pipeline used for the initial processing, QC and management of sequencing data within the Bioinformatics Core Facility at the University of Manchester.
overview requirements install configuration
Starting an analysis <using/setup> Fastq generation <using/make_fastqs> Setting up projects <using/setup_analysis_dirs> Running QC <using/run_qc> Publishing QC <using/publish_qc> Archiving analyses <using/archive> Troubleshooting <using/troubleshooting>
Reporting analyses <using/report> Managing and sharing data <using/managing_data> Importing projects </using/import_project> Running QC stand-alone <using/run_qc_standalone>
10x Genomics single cell data <single_cell/10x_single_cell> Parse Evercode data <single_cell/parse> Takara Bio ICELL8 data <single_cell/icell8>
10x Genomics Visium data <spatial/10x_visium>
Sample sheet manipulations <using/samplesheet>
projects.info <control_files/projects_info> 10x_multiome_libraries.info <control_files/10x_multiome_libraries_info> 10x_multi_config.csv <control_files/10x_multi_config_csv>
Analysis and project directories <output/analysis_dirs> Processing QC <output/processing_qc> Barcode analysis <output/barcode_analysis> QC reports <output/qc_reports>
reference/commands reference/utilities reference/qc_protocol_specification
developers/update_cellranger developers/api_docs/index