NestLink-pipeline

NestLink-pipeline is a pipeline for processing NestLink libraries sequenced by nanopore sequencing. Reads are binned according to their flycodes (UMIs). Accurate consensus sequences are calculated using Medaka. Variants are called with the pipeline, resulting in a flycode assignment table that links protein variants to their respective set of flycodes.

Warning

NestLink-pipeline is still in development. Certain library-specific strings are still hard-coded in main.nf and have to be edited before running the pipeline.

Requirements

Local and cluster execution

• Mamba/ Conda (https://conda-forge.org/)
• Nextflow (Installation guide)
• mini_align (mini_align.sh placed in projectDir/bin/)

Cluster execution only

• Slurm workflow manager
• Singularity

Running the pipeline on the s3it cluster

1. Clone the repository.
2. Edit the params.json file, specify the nanopore reads (bam) and reference sequence.
3. Run the pipeline: sbatch run_NL-pipeline.slurm

Running the pipeline locally

Note

Consensus sequence generation with medaka has to be run manually.

1. Prepare the pipeline as described above.
2. Run the pipeline: bash run_NL-pipeline.sh