analyze genomes using RGI from list provided

[raphenya]

No description provided.

[raphenya]

• add list
• analyze using RGI

[boasvdp]

Hi Amos,

Here is the list (tsv) of FDA-ARGOS genomes. I have filtered them by ESKAPE pathogens and complete genomes. I can cross reference this with Illumina SRA entries if that helps

ESKAPE_FDA-ARGOS_complete_genomes.txt

[raphenya]

@boasvdp Is ok to add the script you used to get ESKAPE_FDA-ARGOS_complete_genomes.txt

[raphenya]

The RGI (https://github.com/arpcard/rgi) results for FDA-ARGOS genomes: results.zip

[jrober84]

I have filtered some of the genomes from the original set since they were not actually complete. These genomes have been run through the MOB-suite to label the different accessions as chromosome
2021-11-12-Genomes.txt
te

[jrober84]

I have updated the datasheet to remove two genomes which the raw reads clearly are not from the closed assembly as well as added in mlst info
2021-11-12-Genomes.txt
y

[raphenya]

$ cat 2021-11-12-Genomes.txt | cut -f4 | grep -v "assembly_acs" > assembly_accession_updated.txt
$ datasets download genome accession --inputfile assembly_accession_updated.txt --exclude-gff3 --exclude-protein --exclude-rna