i am downloading the reference sequence for all the species within a given taxon with the command:
esearch -db "nucleotide" -query "txidX[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa
this is supposed to be a chromosome to align my reading against. But how can I visualize the alignment against this reference for instance with IGB if I don't have the annotations files such as GFF? Essentially, the question is: is it possible to create an annotation file from a multifasta file?