Hi, I'm trying to download all high-quality, complete fna nucleotide fasta genomes for E coli from RefSeq onto a server for further genome analysis. However, I only want the fasta files that come from the main E coli chromosome, with NO plasmids. Since I'm trying to download many genomes, I'd like to do this through a linux terminal (though I wouldn't mind just running a python script as well) but I'm not sure how to proceed with this. Is there a way to filter out and obtain only complete/closed high-quality genomes? Any help is appreciated.
Thanks
1 answer
Okay, so I think I got it figured out. I used a perl script from this GitHub and managed to download all 1935 complete RefSeq genomes for E. coli.
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