What Next After Contigs?

Question

[Smandape]

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?

Answer 1

[sentausa]

Did you try to find its 16S rRNA sequence and BLAST it at NCBI? You might find a closely related bacterium that has its genome sequenced as your reference genome.