• This pipeline performs de novo genome assembly using HiCanu and integrates with nf-core/pairgenomealign for downstream analysis.

• Nextflow
• Slurm environment
• Miniforge
• nf-core

1. Clone the repository:

   git clone https://github.com/connor122721/obtusa
   cd obtusa

To run the de novo assembly pipeline, use the following command:

nextflow run main.nf -profile slurm

This command executes the main.nf script using the Slurm profile defined in nextflow.config. The pipeline will:

1. Read HiFi reads from the specified FASTQ file.
2. Perform genome assembly using HiCanu.
3. Output the assembled genome to the obtusa_hifi/genome directory.

To download genomes using the download_NCBI module, execute the modules/download.nf script:

nextflow run modules/download.nf -profile slurm

This will download genomes based on the species list provided in params.species_list in the nextflow.config file and place the output in the obtusa_hifi/ncbi directory.

After downloading the necessary genomes, you can run the nf-core/pairgenomealign pipeline for comparative genomics analysis.

nf-core/pairgenomealign requires a specific input format. Create a CSV file:

sample,fasta
sample1,/path/to/reference.fasta(or fna)
sample2,/path/to/reference.fasta(or fna)

Run the nf-core/pairgenomealign pipeline using the following command:

nextflow run nf-core/pairgenomealign \
    -r 1.0.0 \
    -profile slurm,apptainer \
    --input samplesheet.csv \
    --target obtusa_hifi/genome/obtusa_hifi/obtusa.contigs.fasta \
    --outdir obtusa_hifi/ \
    -c nextflow.config

After running the scaffolding software, longstitch, test the alignment again:

nextflow run nf-core/pairgenomealign \
    -r 1.0.0 \
    -profile slurm,apptainer \
    --input samplesheet.csv \
    --target obtusa_hifi/longstitch/obtusa_draft.k32.w100.tigmint-ntLink.longstitch-scaffolds.fa \
    --outdir obtusa_hifi_scaffold/ \
    -c nextflow.config

The nextflow.config file contains various parameters that can be adjusted.