Examples

Download tables

Starting from version 0.8.0, you can restrict outputs to assembly_summary.tsv and taxonomy.tsv

• Command

assembly_finder -i staphylococcus_aureus -nb 1 --summary

• Output

📂staphylococcus_aureus
 ┣ 📂logs
 ┃ ┣ 📂taxons
 ┃ ┃ ┗ 📜staphylococcus_aureus.log
 ┃ ┗📜lineage.log
 ┣ 📜assembly_finder.log
 ┣ 📜assembly_summary.tsv
 ┣ 📜config.yaml
 ┗ 📜taxonomy.tsv

Download genomes

Small datasets

• Staphylococcus aureus reference genome

assembly_finder -i staphylococcus_aureus -nb 1

Note

By default, assembly_finder limits genomes to reference or representative

• Any Staphylococcus aureus genome

assembly_finder -i staphylococcus_aureus -nb 1 --reference false

• Download from a list of taxa

assembly_finder -i 1290,1813735,114185 -o taxa -nb 1

• Download using a taxa table

taxa.tsv

taxon	nb
1290	1
1813735	1
114185	1

assembly_finder -i taxa.tsv

Big datasets

Warning

These examples are for big datasets downloads, so using an NCBI api-key is highly recommended

• Download all chlamydia genomes

assembly_finder -i chlamydia --api-key <api-key>

• Best ranking genome for each bacteria species

assembly_finder -i bacteria --api-key <api-key> --rank species --nrank 1

• Complete RefSeq bacteria viruses and archaea (excluding MAGs and atypical)

assembly_finder -i bacteria,viruses,archaea --api-key <api-key> \
--source refseq --assembly-level complete --mag exclude --atypical \
-o outdir

• Specific bioproject

assembly_finder -i PRJNA289059 --api-key <api-key> --accession

Download other files (cds, proteins, gff3 ...)

assembly_finder -i staphylococcus_aureus -nb 1 \
--include genome,rna,protein,cds,gff3,gtf,gbff,seq-report

Output:

📂staphylococcus_aureus
 ┣ 📂download
 ┃ ┣ 📂GCF_000013425.1
 ┃ ┃ ┣ 📜GCF_000013425.1_ASM1342v1_genomic.fna.gz
 ┃ ┃ ┣ 📜cds_from_genomic.fna.gz
 ┃ ┃ ┣ 📜genomic.gbff.gz
 ┃ ┃ ┣ 📜genomic.gff.gz
 ┃ ┃ ┣ 📜genomic.gtf.gz
 ┃ ┃ ┗ 📜protein.faa.gz
 ┃ ┃ ┗ 📜sequence_report.jsonl 
 ┃ ┗ 📜.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