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isoseq3

This is a nextflow implementation of Pacific Biosciences IsoSeq3.1 pipeline.

Setup

Requirements

This pipeline requires anaconda. The required dependencies will then be installed by nextflow into a conda virtual environment

Configuration

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.

Workflow of the pipeline

  1. circular consensus calling
  2. primer removal
  3. refine reads
  4. merge samples (optional)
  5. cluster reads
  6. polish reads
  7. align transcripts (optional)

Run the pipeline

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/*/