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December 04, 2017 / by Wiktor Kuśmirek

Lambda phage de novo assembling!

Since mid-November we became an Nanopore-enabled laboratory. So let’s start sequencing!

The first sequencing experiment was recommended by Oxford Nanopore to familiarise yourself with the device, the equipment and the output data file format. The experiment was based on sequencing a small viral genome called Lambda phage and comparing results against a reference genome to check that the whole process was fine.

As a result of sequencing we obtained over 36 thousands of reads. The accuracy of the reads was about 89.4% and the average identity to the reference was equal to 95.6%. A large number of DNA reads allowed to cover the whole investigated genome by nanopore DNA reads.

alignment reads to reference

Next, we used Canu application to do de novo assembling. As a result, we received only one sequence of length 47852 bp.

Later, we found reference sequence of investigated genome and compared our result with expected DNA sequence. The identity was about 98.4%. However, we obtained some indels (1.4%) and SNPs (0.2%), but we believe, that the differences are caused by natural diversity between reference organism and sequenced sample. A fragment of the alignment result sequence against a reference genome is shown below.

alignment resultant sequence to reference

In the near future we will be sequencing yeast genome, the experiment and the results will be reviewed in the future blog post!