This is a nextflow implementation of Pacific Biosciences IsoSeq3.1 pipeline.
This pipeline requires anaconda. The required dependencies will then be installed by nextflow into a conda virtual environment
The current pipeline is designed to run on the Mendel cluster of the GMI Vienna. To make it run for your group edit the projectName
& fasta
parameters in the the mendel.config file to fit to your group project and needs. To make it run on another infrastructure simply add a new nextflow config file in the conf folder and source via the nextflow.config file. See here for more information.
- circular consensus calling
- primer removal
- refine reads
- merge samples (optional)
- cluster reads
- polish reads
- align transcripts (optional)
To run the pipeline simply run e.g:
nextflow run_isoseq3.nf --input "/lustre/scratch/users/falko.hofmann/isoseq/samples/*/" --output "/lustre/scratch/users/falko.hofmann/isoseq/results/*/