assembly_finder

assembly_finder is a Snakemake-powered cli, written in Snaketool, to download genomes with NCBI datasets.

⚡ Quick start

Installation

Conda

conda create -n assembly_finder assembly_finder

Note

Miniforge is the recommended conda-based distribution

Apptainer

apptainer pull docker://ghcr.io/metagenlab/assembly_finder:latest

Usage

Conda

assembly_finder -i staphylococcus_aureus -nb 1

Apptainer

apptainer run docker://ghcr.io/metagenlab/assembly_finder:latest \
assembly_finder -i staphylococcus_aureus -nb 1 --no-use-conda

Note

set --no-use-conda when running in a container

Output

📂staphylococcus_aureus
 ┣ 📂download
 ┃ ┣ 📂GCF_000013425.1
 ┃ ┃ ┗ 📜GCF_000013425.1_ASM1342v1_genomic.fna.gz
 ┃ ┗ 📜.snakemake_timestamp
 ┣ 📂logs
 ┃ ┣ 📂taxons
 ┃ ┃ ┗ 📜staphylococcus_aureus.log
 ┃ ┣ 📜archive.log
 ┃ ┣ 📜lineage.log
 ┃ ┣ 📜rsync.log
 ┃ ┗ 📜unzip.log
 ┣ 📜archive.zip
 ┣ 📜assembly_finder.log
 ┣ 📜assembly_summary.tsv
 ┣ 📜config.yaml
 ┣ 📜sequence_report.tsv
 ┗ 📜taxonomy.tsv

📚 Documentation

You can find more information on assembly_finder's inputs, outputs and example commands in the documentation

📜 Help

Citation

Please consider citing assembly_finder if you use it in your work.

Farid Chaabane, Trestan Pillonel, Claire Bertelli, MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation, Bioinformatics, 2024;, btae760, https://doi.org/10.1093/bioinformatics/btae760

@article{chaabane_mess_2024,
	title = {MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation},
	issn = {1367-4811},
	url = {https://doi.org/10.1093/bioinformatics/btae760},
	doi = {10.1093/bioinformatics/btae760},
	journal = {Bioinformatics},
	author = {Chaabane, Farid and Pillonel, Trestan and Bertelli, Claire},
	month = dec,
	year = {2024},
	pages = {btae760},
}