The Scaffolds file should contain nucleotide sequences in a fasta format.
Each sequence should correspond to a scaffold or a chromosome and should look like similar to this:
Scaffolds should be long sequences corresponding approximately
to complete chromosomes. Each sequence in the Scaffolds file should
correspond to several contigs separated by runs of NNNNNN nucleotides.
The total number of scaffolds should be less than or equal to 702.
Only A,T,C,G,N nucleotide symbols can be processed by YGAP (upper or lowercase is fine). If your fasta file contains ambiguous nucleotide symbols (i.e. R,Y,S,W,K,M,B,D,H,V) they should be replaced for Ns before uploading to YGAP.