reference genomes in samestr extract command

[qinglong89]

The module samestr extract obtains MetaPhlAn marker sequences from reference genomes by using BLASTN. samestr extract \ --input-files reference_genomes/*.fasta \ --marker-dir marker_db/ \ --nprocs 30 \ --output-dir out_extract/

My question: where should we download the reference genomes? this is not clear to me.

Thanks!

[qinglong89]

NCBI refseq genomes?

ncbi-genome-download --section refseq --format fasta --parallel 80 bacteria

[danielpodlesny]

Yes, for example from NCBI or proGenomes. samestr extract will extract the marker regions from the genome which can be compared and studied across genomes and metagenomes. Use samestr convert for dealing with metagenomes.

Hope this helps!