Atlas assembler

Tool to assemble long reads eg. ONT

Pipeline information

• Author(s): Fabian Landman, Sohana Singh
• Organization: Rijksinstituut voor Volksgezondheid en Milieu (RIVM)
• Department: Infectieziekteonderzoek, Diagnostiek en Laboratorium Surveillance (IDS), Bacteriologie (BPD)
• Start date: 01 - 04 - 2025
• Commissioned by: Casper Jamin

About this project

Short description of the pipeline.

Prerequisities

• Linux-like environment with (mini) conda installed
• Python3.11.11

Installation

1. Clone the repository.

git clone [link]

2. Go to [name] directory.

cd atlas-assembler

3. Continue steps

Parameters & Usage

Command for help

• -h, --help Shows the help of the pipeline

Required parameters

• --sequencing-tech 'illumina' or 'nanopore' The default is illumina.

The base command to run this program.

python atlas_assembler.py -i [dir/to/fasta_or_fastq_files] -o [output/dir] --sequencing-tech nanopore

Detailed information about the pipeline can be found in the [documentation](link to other docs). This documentation is only suitable for users that have access to the RIVM Linux environment.

Explanation of the output

• log: Log with output and error file from the cluster for each Snakemake rule/step that is performed
• output_dir_1 Explanation of the output in this directory

Issues

• For now this only works on the RIVM cluster.
• Place to store the issues that are not resolved yet.

Future ideas for this pipeline

• Make this pipeline available and user friendly for users outside RIVM.
• Place to store future ideas.

License

This pipeline is licensed with a AGPL3 license. Detailed information can be found inside the 'LICENSE' file in this repository.

Contact

• Contact person: Sohana Singh
• Email [email protected]

Acknowledgements