Nextflow pipeline for analysing (Illumina) 2x300bp nanobody sequencing data. Performs pre-processing and automatically generates a basic analysis report.

⭐ Before running the pipeline, make sure to edit the nextflow.config file to suit your system and point to the correct input and output directories.

⭐ For detailed usage instructions, check out the documentation website

The quickest way to run alpseq is by running the command below (after editing the nextflow.config file):

nextflow run ./main.nf -profile <docker or singularity> 

Or by running it through the seqera cloud platform's GUI.

• Our documentation website

• The alpseq preprint

• The data published alongside alpseq