Sequencing analysis pipeline (aqueduct) for validating plasmids and DNA assembly constructs, using long reads.
Pull the Nextflow pipeline:
nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.3.0
Pull the Docker image that contains the required software (requires access to EGF's container repo):
docker pull ghcr.io/edinburgh-genome-foundry/sequeduct:latest
Alternatively, build the image locally from the cloned repo:
docker build . -f containers/Dockerfile --tag sequeduct_local
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 v0.3.0 -entry preview --fastq_dir='fastq' \
--reference_dir='genbank' \
--sample_sheet='sample_sheet.csv' \
-profile docker
# Analysis
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.0 -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 v0.3.0 -entry review --reference_dir='genbank' \
--results_csv='results_sheet.csv' \
--projectname='EGF project review' \
--all_parts='parts_fasta/part_sequences.fasta' \
--assembly_plan='assembly_plan.csv' \
-profile docker
# De novo assembly
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.0 -entry assembly --fastq_dir='fastq' \
--results_csv='assembly_sheet.csv' \
-profile docker
The above commands each output a directory within a created results
directory. Similarly, Nextflow creates and uses a directory named work
, so ensure that your project directory doesn't have a directory with the same name. 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. The Review pipeline utilises the output files of the Analysis pipeline, but otherwise the pipelines are independent. Please find example sheets in the examples
directory.
A more detailed example and demonstration data are available at the Sequeduct demo site.
Use -with-docker sequeduct_local
to use a locally built Docker image (instead of -profile docker
).
For simplicity, the names in the sample sheet are used for finding the reference Genbank files, therefore sample names must match filenames with a ".gb" extension.
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
).
Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
Sequeduct was written at the Edinburgh Genome Foundry by Peter Vegh, and is released under the GPLv3 license.