getfasta bedtools from NDARO

Question

[Elham]

Hi, I want to extract a huge number of nucleotide sequences from my database downloaded from NDARO. I am going to use bedtools getfasta command. I have prepared a bed file containing Contig id, Stat, Stop and Strand to extract fasta sequences. However, I need some guidance. What reference genome fasta should I use? I have about 122,000 samples to extract sequences. Thank you