Starting a new year of Sequence a genome!
We have selected 3 bacterial strains isolated from contaminated ground water, all from the same species. The students have grown the bacteria, isolated the DNA, and brought it to our sequencing facility. They don’t get to do the final library preparation themselves, but they do get a guided tour of our sequencing machines: Illumina HiSeq and MiSeq, PacBio and IonTorrent.
And now the sequencing is done, and the students are ready to assemble: 4.5, 5.3 and 6.3 million reads, respectively for each of our three bugs.
In preparation for this difficult exercice, we had the hardest session of the year: Introduction to Unix and using the cluster! This will allow them to perform the quality control and assembly steps on our 16 million reads. The students will test different assemblers, quality control cut-offs, and k-mer sizes, which will hopefully allow us to select the best assembly for each of the three strains by the end of this semester.