Skip to main content

nf-core/pixelator is an analysis pipeline for analysis of Molecular Pixelation assays.

The pipeline is build using the Nextflow workflow manager and is developed as a part of nf-core.

What is Nextflow

Nextflow is a workflow manager. It implements a Domain Specific Language (DSL) that simplifies the implementation and running of workflows on cloud or high-performance computing (HPC) infrastructures. It enables the writing of scalable and reproducible scientific workflows. It can integrate various software package and environment management systems such as Docker, Singularity, and Conda. It allows for existing pipelines written in common scripting languages, such as R and Python, to be seamlessly coupled together.

By using Nextflow, Molecular Pixelation assays can be processed across a wide variety of HPC Batch systems, cloud computing platforms, and local computing clusters in a reproducible manner. The nf-core community maintains a set of ready-made configurations for institutional HPC infrastructures.

We use the name nf-core/pixelator for the Nextflow pipeline that uses pixelator to process sequencing data to MPX files ready for analysis. The pixelator library is also the name of the software suite that Pixelgen Technologies uses to analyze MPX data in Python.

What is nf-core

nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. nf-core provides a set of guidelines, tools and infrastructure to build best-practice nextflow pipelines for the bioinformatics community.

Being part of the nf-core community ensures that the pipeline is well tested and easy to use for people familiar with other nf-core pipelines.

Pipeline overview

The nf-core/pixelator pipeline will follow the steps below to process your sequencing data.

  1. Build amplicon from input reads (pixelator amplicon)
  2. Read QC and filtering, correctness of the pixel binding sequence sequences ( pixelator preqc & pixelator adapterqc)
  3. Assign a marker (barcode) to each read (pixelator demux)
  4. Error correction, duplicate removal, compute read counts (pixelator collapse)
  5. Compute the components of the graph from the edge list in order to create putative cells (pixelator graph)
  6. Call and annotate cells (pixelator annotate)
  7. Analyze the cells for polarization and colocalization (pixelator analysis)
  8. Report generation (pixelator report)

The nf-core/pixelator pipeline coordinates the execution through these different stages of analysis while providing useful monitoring and debugging logs as well as restarting utilities.