Introduction

Pixelgen Technologies provides Pixelator, a suite of open source software solutions that empower users working with Molecular Pixelation (MPX) and Proximity Network (PNA) assays in data processing and analysis.

Pixelator can be used in two ways: as a data processing pipeline (nf-core/pixelator) and as a programming library (pixelator). The pipeline nf-core/pixelator consists of several steps and will produce ready-to-analyze outputs from your initial FASTQ sequencing libraries. Usage of Pixelator as a programming library is covered in our data analysis sections for MPX and PNA.

Pixelator Architecture

The pipeline nf-core/pixelator performs a series of steps using the pixelator command-line tool.

The pipeline nf-core/pixelator is built using Nextflow - a workflow tool that enables task execution across multiple computing infrastructures. The use of Docker containers ensures effortless installation and reproducible results. This design enables compatibility with various infrastructures and cloud environments. nf-core is particularly useful, as it supports a wide range of institutional HPC infrastructures.

When using nf-core/pixelator on your platform, nextflow will download the pipeline from the nf-core repository the first time it is run. If the pipeline has already been run, a local copy will be reused. After this initial download, the nf-core/pixelator pipeline will download any containers it needs to execute the pipeline. These containers provides the software required to process raw FASTQ reads into analysis-ready results. Nextflow will coordinate the execution of these stages and provides useful monitoring, debugging logs, and restart capabilities.