AlphaSquad
commented
6 years ago Hi, let me try to answer your questions:
- the only thing you really need to download is the genome sequence (the *.fna.gz file). The gff file is only required, if you want so artificially add strains to your data set, if you don't want to do that then you can leave the id_to_gff field empty. The id_to_genome_file field expects a file which, tab-separated, expects a genome ID and the path; if you only want to use that single genome that file would for example look like this:
GCF_000006825\t/path/to/GCF000006825.fnaThe '\t' in this string, as well as in the metadata file string you wrote stands for "tab-separated" files (.tsv), where the individual fields are separated by a single Tab. - The genome ID is just a name you can give to your genome, you can choose GCF000006825 for example, you just need to make sure that the IDs are consistent between the metadata and the genome_to_id files.
An OTU (Operational Taxonomic Unit) is a definition to classify groups of related genomes. If you have two genomes which are closely related to each other, these should get the same OTU. This can be any string (or number). If you don't care for genomic relationships you can give every genome its own OTU (e.g. its genome ID) or can give every genome the same OTU (e.g. 0).
The novelty category is a measure of novelty of your genome in case you do not use published genomes for simulating metagenomes, i.e. if you are using a genome which was classified as being of a genus which has not been described before, the novelty category would be "new_genus". Since you are using database genomes I suggest setting this to "known_strain" for every genome.
The NCBI ID you found looks correct to me, all the other fields have to be set by you yourself, the file might look like this:
genome_ID\tOTU\tNCBI_ID\tnovelty_category GCF_000006825\t0\t272843\tknown_strain
I hope this helps. If there is anything more, feel free to comment or write a mail.
kmin940
Hi, I'm trying to simulate a dataset using CAMISIM but since I am relatively new to metagenomics, I do not have clear understandings on some names. My questions are :
1) I want to use genome with ncbi accession GCF_000006825.1, so I visited ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/825/GCF_000006825.1_ASM682v1 From this site, do I only need to download GCF_000006825.1_ASM682v1_genomic.fna.gz (genome sequence) GCF_000006825.1_ASM682v1_genomic.gff.gz (genome annotation) and add the paths to id_to_genome and id_to_gff respectively?
2) I'm not sure what these 4 fields mean for metadata. i.e. Row 1 (header): genome_ID\tOTU\NCBI_ID\tnovelty_category What is genome ID for GCF_000006825.1? Where can I find this information? What is tOTU for GCF_000006825.1? Where can I find this information? I found from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=272843 that taxonomy identifier for GCF_000006825.1 is 272843. What should I put for tnovelty_category?
It would also be great if you can provide some other concrete example genome with the corresponding genome_ID\tOTU\NCBI_ID\tnovelty_category. Thank you very much for your help.