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.

Developer Documentation