This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to circularise the bacterial genome?

We have sequenced a bacterial genome (illumina paired end sequencing) and assembled by SPAdes (denovo assembly). Further, I would like to view the assembled genome through BRIG viewer. BRIG support completed genome/circular genome or Mauve contig reordered draft genome (contig reordered based on reference genome). Since, my genome of interest do not have reference genome, so I could not proceed Mauve for contig reordering. Therefore, Is there any way to do the same.

Thanks in advance.

assembly genome next-gen brig
• 1,546 views • link
updated by Ram Ram • written by Kumar Kumar

1 answer

You don't need to circularise for BRIG. There is a bug in it that stops it correctly handling multifasta files however. Since you don't know the true order of contigs without a reference genome, you can just strip out the contig headers and concatenate them all together.

You cannot truly circularise the sequence unless you have terminal overlaps, and sufficient sequencing to yield a closed chromosome, which you will very likely not have from illumina.

• 0 views • link
written by Joe Joe

Log in to answer this question.

More posts like this