This folder contains scripts for generating and evaluating assemblies of genomes using long-read Oxford Nanpore sequencing. It uses the data flow programming language nextflow to coordinate the steps in the pipeline, which involves:
- Automated QC of long-read genomic sequences (and Illumina reads for polishing)
- Assessment of contamination
- De novo or reference-guided assembly with different assemblers and parameters
- Automated assessment of the assembly
Docker, singularity, etc.
nextflow run [pipeline.nf]
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