auto-process-ngs: automated processing of NGS data
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
- Installation
- Configuration
- Overview
- Basic configuration
- Sequencers and platforms
- Default metadata
- Job Runners
- Setting number of available CPUs
- Running on a compute cluster
- Managing concurrent jobs and process loads
- Using environment modules
- Using conda to resolve pipeline dependencies
- Specifying BCL to Fastq conversion software and options
- QC pipeline configuration
- Data transfer destinations
- Bash tab completion
- Reporting analyses
- Managing and sharing data
manage_fastqs.py
: managing and copy Fastq filestransfer_data.py
: copying data for transfer to end usersdownload_fastqs.py
: fetch Fastqs from a webserver in batchupdate_project_metadata.py
: manage metadata associated with a projectaudit_projects.py
: auditing disk usage for multiple runs- Exporting Fastqs to a data library in a local Galaxy instance
- Importing projects
- Running QC stand-alone
auto_process
commands- Utilities
- analyse_barcodes.py
- assign_barcodes.py
- audit_projects.py
- build_index.py
- concat_fastqs.py
- barcode_splitter.py
- download_fastqs.py
- demultiplex_icell8_atac.py
- fastq_statistics.py
- icell8_contamination_filter.py
- icell8_report.py
- icell8_stats.py
- manage_fastqs.py
- process_icell8.py
- run_qc.py
- split_icell8_fastqs.py
- transfer_data.py
- update_project_metadata.py
- QC protocol specification
- Updating CellRanger
- Developers’ API documentation
auto_process_ngs.analysis
auto_process_ngs.applications
auto_process_ngs.auto_processor
auto_process_ngs.barcodes
auto_process_ngs.barcodes.analysis
auto_process_ngs.barcodes.pipeline
auto_process_ngs.barcodes.splitter
auto_process_ngs.bcl2fastq
auto_process_ngs.bcl2fastq.pipeline
auto_process_ngs.bcl2fastq.reporting
auto_process_ngs.bcl2fastq.utils
auto_process_ngs.cli
auto_process_ngs.cli.auto_process
auto_process_ngs.cli.build_index
auto_process_ngs.cli.reportqc
auto_process_ngs.cli.run_qc
auto_process_ngs.cli.transfer_data
auto_process_ngs.command
auto_process_ngs.commands
auto_process_ngs.commands.analyse_barcodes_cmd
auto_process_ngs.commands.archive_cmd
auto_process_ngs.commands.clone_cmd
auto_process_ngs.commands.import_project_cmd
auto_process_ngs.commands.make_fastqs_cmd
auto_process_ngs.commands.merge_fastq_dirs_cmd
auto_process_ngs.commands.publish_qc_cmd
auto_process_ngs.commands.report_cmd
auto_process_ngs.commands.run_qc_cmd
auto_process_ngs.commands.samplesheet_cmd
auto_process_ngs.commands.setup_analysis_dirs_cmd
auto_process_ngs.commands.setup_cmd
auto_process_ngs.commands.update_cmd
auto_process_ngs.commands.update_fastq_stats_cmd
auto_process_ngs.conda
auto_process_ngs.config
auto_process_ngs.conftest
auto_process_ngs.css_rules
auto_process_ngs.decorators
auto_process_ngs.docwriter
auto_process_ngs.exceptions
auto_process_ngs.fastq_utils
auto_process_ngs.fileops
auto_process_ngs.icell8
auto_process_ngs.icell8.atac
auto_process_ngs.icell8.constants
auto_process_ngs.icell8.pipeline
auto_process_ngs.icell8.utils
auto_process_ngs.indexes
auto_process_ngs.metadata
auto_process_ngs.mock
auto_process_ngs.mock10xdata
auto_process_ngs.mockqc
auto_process_ngs.mockqcdata
auto_process_ngs.pipeliner
auto_process_ngs.qc
auto_process_ngs.qc.cellranger
auto_process_ngs.qc.constants
auto_process_ngs.qc.fastq_screen
auto_process_ngs.qc.fastq_stats
auto_process_ngs.qc.fastq_strand
auto_process_ngs.qc.fastqc
auto_process_ngs.qc.outputs
auto_process_ngs.qc.picard
auto_process_ngs.qc.pipeline
auto_process_ngs.qc.plots
auto_process_ngs.qc.protocols
auto_process_ngs.qc.qualimap
auto_process_ngs.qc.reporting
auto_process_ngs.qc.rseqc
auto_process_ngs.qc.seqlens
auto_process_ngs.qc.utils
auto_process_ngs.qc.verification
auto_process_ngs.samplesheet_utils
auto_process_ngs.settings
auto_process_ngs.simple_scheduler
auto_process_ngs.stats
auto_process_ngs.tenx
auto_process_ngs.tenx.cellplex
auto_process_ngs.tenx.metrics
auto_process_ngs.tenx.multiome
auto_process_ngs.tenx.utils
auto_process_ngs.utils