De novo community design: Genomes download

[Shahab-Sa]

Hi,
I am trying to design a de novo community consisting of numerous bacterial species using NCBI taxonomy identifiers. I have modified the required genome_to_id.tsv, metadata.tsv, abundance.tsv and mini_config.ini.

I am confused in the process of preparing bacterial genomes to put in the /defaults/genomes folder.
Is there any script in the CAMISIM pipeline which downloads those genomes during the run?
As you know, it is not feasible to download them one by one!
Thanks in advance.

[AlphaSquad]

Hi,
thank you for your interest in CAMISIM. Indeed you are expected to somehow have acquired the genomes you want to use for a de novo run of CAMISIM in beforehand. For the NCBI it is fortunately relatively easy to batch download genomes (and the from profile mode of CAMISIM does make use of that). You can use the Entrez API for doing so: https://www.ncbi.nlm.nih.gov/sites/batchentrez
A mapping from tax ids to genomes is available on the NCBI ftp server: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/
or a snapshot used for the creation of the CAMISIM data sets can be found within CAMISIM: tools/assembly_summary_complete_genomes.txt

[Shahab-Sa]

Thanks for your support.