Skip to content

Examples

Download summary tables

Starting from v0.8.0, you can restrict outputs to assembly_summary.tsv and taxonomy.tsv

  • Command
assembly_finder -i staphylococcus_aureus --reference --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 complete genomes
assembly_finder -i staphylococcus_aureus

Note

By default, assembly_finder searches assembly levels in the following order: complete, chromosome, scaffold, and contig.

The search stops at the first assembly level where genomes are found.

This behavior was introduced in v0.9.0 to allow finding the best genomes available for each taxon

  • All Staphylococcus aureus genomes 
assembly_finder -i staphylococcus_aureus --all

Note

The --all option disables the default iteration over assembly levels. When used, all genomes for the specified taxon are downloaded, regardless of their assembly level.

  • Any Staphylococcus aureus complete genome
assembly_finder -i staphylococcus_aureus -nb 1

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 --all --api-key <api-key>
  • Best ranking complete genome per bacteria species
assembly_finder -i eubacteria --api-key <api-key> --rank species --nrank 1
  • Complete bacteria viruses and archaea genomes from RefSeq (excluding MAGs and atypical)
assembly_finder -i eubacteria,viruses,archaea \
--api-key <api-key> \
--source refseq \
--mag exclude \
-o outdir
  • Specific bioproject
assembly_finder -i PRJNA289059 --api-key <api-key> --accession

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

assembly_finder -i staphylococcus_aureus --reference \
--include 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