I have contigs from a bacterial genome sequence. I am trying to find what would be the reference for this strain or where does it belong to in the phylogenetic tree. Also, what would be a good way to stitch them together? I did BLAST with individual contigs and also with all contigs together but I am not sure if this is the correct way to determine which is the closest strain from the available ones in NCBI.
Any thoughts about how should one proceed without a reference?