Deprecated: The example is now part of the main repository.

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DENTIST: Mini Example

A small example to test DENTIST's workflow

Quickly test DENTIST with this example workflow. It uses part of the D. melanogaster reference assembly (dm6) and simulated reads to demonstrate the workflow. The full source code of DENTIST is available at https://github.com/a-ludi/dentist.

If you experience issues, please search the issues at DENTIST's repository or create a new one if you cannot find an answer to your problem.

Table of Contents

• Install
• Usage
• Troubleshooting
• Citation
• Maintainer
• Contributing
• License

Install

Make sure you have Snakemake 5.32.1 or later installed.

You can also use the convenient Singularity container to execute the rules. Just make sure you have Singularity 3.5.x or later installed.

Usage

First of all download the test data and workflow and switch to the dentist-example directory.

wget https://github.com/a-ludi/dentist-example/releases/download/v2.0.0-3/dentist-example.tar.gz
tar -xzf dentist-example.tar.gz
cd dentist-example

Local Execution

Execute the entire workflow on your local machine using all cores:

# run the workflow
PATH="$PWD/bin:$PATH" snakemake --configfile=snakemake.yml --cores=all

# validate the files
md5sum -c checksum.md5

Execution takes approx. 7 minutes and a maximum of 1.7GB memory on my little laptop with an Intel® Core™ i5-5200U CPU @ 2.20GHz.

Use Conda

Make sure Conda is installed on your system. You can then use DENTIST like so:

# run the workflow
snakemake --configfile=snakemake.yml --use-conda --cores=all

# validate the files
md5sum -c checksum.md5

Execution in Singularity Container

Execute the workflow inside a convenient Singularity image by adding --use-singularity to the call to Snakemake:

# run the workflow
snakemake --configfile=snakemake.yml --use-singularity --cores=all

# validate the files
md5sum -c checksum.md5

Cluster Execution

Execute the workflow on a SLURM cluster:

mkdir -p "$HOME/.config/snakemake/slurm"
# select one of the profile-slurm.{drmaa,submit-async,submit-sync}.yml files
cp -v "profile-slurm.sync.yml" "$HOME/.config/snakemake/slurm/config.yaml"
# execute using the cluster profile and conda
snakemake --configfile=snakemake.yml --use-conda --profile=slurm

# validate the files
md5sum -c checksum.md5

If you want to run with a different cluster manager or in the cloud, please read the advice in [DENTIST's README][dentist-cluster]. The easiest option is to adjust the srun command in profile-slurm.sync.yml to your cluster, e.g. qsub -sync yes. The command must submit a job to the cluster and wait for it to finish.

Citation

Arne Ludwig, Martin Pippel, Gene Myers, Michael Hiller. DENTIST – using long reads to close assembly gaps at high accuracy. Submitted for peer review. Pre-print at https://doi.org/10.1101/2021.02.26.432990

Maintainer

DENTIST is being developed by Arne Ludwig <ludwig@mpi-cbg.de> at the Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

License

This project is licensed under MIT License (see LICENSE).