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Old 03-13-2014, 01:31 PM   #3
Matt Kearse
Location: New Zealand

Join Date: Mar 2014
Posts: 20

The algorithm may produce multiple circular contigs as each contig may independently circularize.

As a quick confirmation I downloaded a random sample of 100 viral genomes, 24 of which are circular. I generated simulated data from them all and mixed it all together.

De novo assembly of this mixed data produced 106 contigs, 6 of them being tiny contigs consisting of reads with errors. The other 100 contigs produced matched the original genomes perfectly apart from a 2 bp uncertainty due to read errors in 1 genome. 77 contigs were linear and 23 were circular in keeping with the original genomes. 1 failed to circularize due to insufficient coverage.
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