Nanoseq Analysis for GOLDOG Longevity Project

This repository contains a Nextflow pipeline for Nanoseq analysis applied to long-read data ( DNA , Blue line) for the GOLDOG longevity project (1st batch).

Prerequisites

Before running the Nextflow command, make sure to perform the following steps:

1. Create an input file (samplesheet.csv)

Create a file named samplesheet.csv with the following information:

group,replicate,barcode,input_file,fasta,gtf

2. Choose a compute cluster node

Use the following command to request a node on the compute cluster: srun --pty --cpus-per-task=12 --mem=100G bash

3. Running the Nanoseq Nextflow Pipeline

Execute the following command to run the Nanoseq Nextflow pipeline:

  --input samplesheet.csv \
  --protocol DNA \
  --skip_quantification \
  --skip_demultiplexing \
  -profile singularity

• --input samplesheet.csv : specifies the input file.
• --protocol DNA: indicates the DNA analysis protocol.
• --skip_quantification: skips the quantification step.
• --skip_demultiplexing: skips the demultiplexing step.
• -profile singularity: uses the Singularity profile for execution.

Ensure that Nextflow is installed, and Singularity is available on your cluster before running the command.

Output

The pipeline generates the following output directories:

• fastqc: FastQC reports for input and output files.
• minimap2: Minimap2 alignment results.
• multiqc: MultiQC report summarizing the analysis.
• nanoplot: NanoPlot reports for input and output files.
• pipeline_info: Information about the pipeline.
• variant_calling: zipped VCF file with smtructural variants.

Analysis

• 2nd_batch : Contains the main second batch analyses
• QC_fastqc : Statistical analysis of quality for the sequences resulting from FastQC.
• QC_mapping : QC_mapping: Statistical analysis of quality for the alignment results with the reference genome.
• QC_concat : Analysis of concatenated 1st batch data.

Environment Path & Versions

• R: /local/env/envr-4.1.3.sh
• samtools: /local/env/envsamtools-1.15.sh
• Python: /local/env/envpython-3.9.5.sh
• Pipeline_info :

  BEDTOOLS_GENOMECOV:
  bedtools: 2.29.2
  CUSTOM_DUMPSOFTWAREVERSIONS:
    python: 3.10.6
    yaml: '6.0'
  CUTESV:
  cuteSV: 1.0.12
  DEEPVARIANT:
    deepvariant: 1.4.0
  GET_CHROM_SIZES:
    samtools: '1.13'
  MINIMAP2_INDEX:
    minimap2: 2.17-r941
  SAMTOOLS_STATS:
    samtools: 1.16.1
  SNIFFLES:
    sniffles: 1.0.12
  UCSC_BEDGRAPHTOBIGWIG:
    ucsc_bedgraphtobigwig: '377'
  Workflow:
    Nextflow: 23.10.0
    nf-core/nanoseq: 3.1.0
  

First batch details