Assembly Finder

Assembly finder is a Snakemake-powered cli to download genomes with NCBI datasets.

Installation

mamba create -n assembly_finder assembly_finder

Example

Command

assembly_finder -i staphylococcus_aureus -nb 1 

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

Usage