Sequencing analysis pipeline (aqueduct) for validating plasmids and DNA assembly constructs, using long reads.

Install Nextflow and Docker.

Set up credentials in the SCM configuration file, then pull the Nextflow image:

nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.2.1

Pull the Docker image that contains the required software:

docker pull ghcr.io/edinburgh-genome-foundry/sequeduct:latest

Create a directory for your project and copy (or link) the FASTQ directories from your Nanopore run (e.g. into fastq). Specify this together with a sample sheet in your commands:

# Preview
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.1 -entry preview --fastq_dir='fastq' --reference_dir='genbank' \
    --sample_sheet='sample_sheet.csv' \
    -profile docker
# Analysis
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.1 -entry analysis --fastq_dir='fastq' --reference_dir='genbank' \
    --sample_sheet='sample_sheet.csv' \
    --projectname='EGF project' \
    -profile docker
# Review
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.1 -entry review --reference_dir='genbank' \
    --results_csv='results_finalised.csv' \
    --projectname='EGF project review' \
    --all_parts='parts_fasta/part_sequences.fasta' \
    --assembly_plan='assembly_plan.csv' \
    -profile docker

The above three commands each output a directory within results. Similarly, Nextflow creates and uses a directory named work, so ensure that your project directory doesn't have one. Specify revision of the project with -r (a git branch or tag), and choose a configuration profile (with -profile). Profiles are specified in the Nextflow config files.

Note that canu v2.2 requires minimum 100 reads, otherwise it returns an error. A fix has been posted, but it's not released yet.

For convenience, a script is included to collect plot files from the result directories (bin/collect_plots.py).

git clone [email protected]:Edinburgh-Genome-Foundry/Ediacara.git
docker build . -f containers/Dockerfile --tag sequeduct_local

Copyright 2021 Edinburgh Genome Foundry

Sequeduct was written at the Edinburgh Genome Foundry by Peter Vegh.