assembly_finder

assembly_finder is a Snakemake CLI wrapper for NCBI datasets, written with Snaketool, for easy genome assembly downloads.

Installation

Conda (recommended)gitApptainer

conda create -n assembly_finder -c bioconda assembly_finder

Note

Requires a Miniforge installation

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

Note

Requires a Miniforge installation

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

Usage

Taxon

• Download staphylococcus aureus reference genome

assembly_finder -i staphylococcus_aureus --reference

or

assembly_finder -i 1280 -r

Taxa

• Find reference genomes for multiple taxa

assembly_finder -i 1290,1813735,114185 --reference

or

assembly_finder -i taxa.txt --reference

with taxa.txt:

1280
1813735
114185

Accessions

• Download staphylococcus aureus reference genome using its assembly accession

assembly_finder --acc -i GCF_000013425.1

• Download multiple accessions

assembly_finder --acc -i GCF_003812505.1,GCF_001618865.1,GCF_000287275.1  

or

assembly_finder -i accessions.txt 

with accessions.txt:

GCF_003812505.1
GCF_001618865.1
GCF_000287275.1

Command-line options