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oist-assembler

This pipeline assembles genomes starting from long-read Oxford Nanopore sequences. It uses the data flow language nextflow to coordinate the steps in the pipeline, which involves:

  • Read-level quality control

  • Basecalling with Guppy

  • Read adapter trimming

  • De novo or reference-guided assembly with different assemblers and parameters

  • Automated assessment of the assembly

Installation

nextflow pull luslab/oist-assembler

To run this pipeline, you will need Nextflow and Docker (or Singularity). If you are planning to use GPU-accelerated basecalling, you'll also need a CUDA-capable GPU and the NVIDIA Container Toolkit.

Test

In this repository clone:

nextflow run main.nf -profile <oist,crick> --input test_workflows/assembly_1.metadata.csv

Use

Directly from GitHub:

nextflow run luslab/oist-assembler -profile <oist,crick> --input [metadata.csv]

In this repository clone:

nextflow run main.nf -config [pipeline.config] --input [metadata.csv]

Something Something

🎉