assembly_finder

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

Installation

Conda (recommended)Apptainergit

conda create -n assembly_finder assembly_finder

Note

Requires a Miniforge installation

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

Note

Add --no-use-conda when using the container

git clone https://github.com/metagenlab/assembly_finder.git
pip install -e assembly_finder

Note

Requires a Miniforge installation

Usage

Command

standardcontainer

assembly_finder -i staphylococcus_aureus -nb 1 

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

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
 ┗ 📜taxonomy.tsv

Command-line options