Analyse variants from nanopore reads

Apply the variant calling pipeline to reads from Nanopore sequencer.

Purpose

• Analyse variants in Nanopore reads

Required inputs

• Single-end reads from Nanopore sequencer in gzipped fastq format
  • Each sample is represented by a single gzipped fastq file
• Reference genome in fasta format

|-- reads/original
        |-- <sample_1>.fastq.gz
        |-- <sample_2>.fastq.gz
|-- reference/<reference>
        |-- <reference>.fa

Generated outputs

• List of identified variants in VCF file, filtered by user-defined criteria
• Summary PDF report to assess quality of reads, mapping and variant calling

Example

How to run example:

cd /usr/local/snakelines/example/nanopore

snakemake \
   --snakefile ../../snakelines.snake \
   --configfile config.yaml \
   --use-conda

Example configuration:

platform: nanopore
sequencing: single_end

samples:
      - name: example_.*
        reference: sars_cov_2

report_dir: report/example
threads: 16

reference:
    index:
        fai:
            method: samtools

reads:
    preprocess:
        trimmed:
            method: trimmomatic
            temporary: False
            crop: 500
            quality: 20
            headcrop: 20
            minlen: 35

    report:
        quality_report:
            method: fastqc
            read_types:
                - original
mapping:
    mapper:
        method: minimap2
    index:
        method: samtools
    postprocess:
        sorted:
            method: samtools
    report:
        quality_report:
            method: qualimap
            map_types:
                - original

variant:
    caller:
        method: clair

lineage:
    caller:
        method: pangolin
    summary:
        method: cat