AG7: closing genomes with PacBio

PacBio CCS reads are long and accurate (error rate around 0.1 %). In addition PacBio provides a very uniform coverage (even for AT rich or GC rich regions) and a random distribution in the pattern of errors along the sequence.  Our system AG7 is able to join illumina contigs using PacBio CCS reads. 

We lengthen illumina contigs and join them based on CCS PacBio reads connecting the ends of two different contigs. The analysis of these connections allows the scaffolding of the illumina contigs and then the final joining of the contigs getting the closing of bacterial genomes.

The strategy of our method is:

-  First to assemble the  illumina reads, obtaining an assembly that

   usually has a high local precision, and then

-  Join the illumina contigs using the CCS PacBio long sequences.

The length of these sequences allows us to solve the main problems of the Illumina read assembly that are the repeats, the non-uniform coverage and the non-random error distribution.

The number of PacBio CCS reads needed to get a sufficient coverage for a bacterial genome is very low due to the length of the reads and to the uniform coverage. So it allows the use of innovative methods and algorithms to manage them.

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