Nextflow nf-core pipeline to generate Molecular Pixelation data with pixelator (Pixelgen Technologies AB)
*nf-core/pixelator* is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays.
It takes a samplesheet as input and will process your data using
pixelator to produce final antibody counts.
- Build amplicon from input reads (
- Read QC and filtering, correctness of the pixel binding sequence sequences (
pixelator preqc | pixelator adapterqc)
- Assign a marker (barcode) to each read (
- Error correction, duplicate removal, compute read counts (
- Compute the components of the graph from the edge list in order to create putative cells (
- Call and annotate cells (
- Analyze the cells for polarization and colocalization (
- Report generation (
First, prepare a samplesheet with your input data that looks as follows:
Each row represents a sample and gives the design, a panel file and the input fastq files.
Now, you can run the pipeline using:
nextflow run nf-core/pixelator \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>
Please provide pipeline parameters via the CLI or Nextflow
-params-file option. Custom config files including those
provided by the
-c Nextflow option can be used to provide any configuration *except for parameters*;
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
nf-core/pixelator was originally written for Pixelgen Technologies AB by:
- Florian De Temmerman
- Johan Dahlberg
- Alvaro Martinez Barrio
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
Citations<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --> <!-- If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
An extensive list of references for the tools used by the pipeline can be found in the
You can cite the
nf-core publication as follows:
*The nf-core framework for community-curated bioinformatics pipelines.*
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.