What Next After Contigs? · Biostar

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What Next After Contigs?

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?

assembly phylogenetics phylogeny contigs

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updated 12.9 years ago by sentausa

• written 12.9 years ago by Smandape

1 answer

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.

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written 12.9 years ago by sentausa

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