Category Archives: assembly

Good assembly of genomes with #PacBio: no difference between our strains

A new year of the class Sequence a genome with our master students has started! In September, the students cultivated two strains likely to be Pseudomonas protegens, extracted their DNA and prepared it for PacBio sequencing. All of the students … Continue reading

Posted in assembly, bioinformatics, experimental, students | Leave a comment

Finishing PacBio assembly, and a presentation by our local PacBio representative

In this first session of the course “Sequence a genome” since we sent DNA to the sequencing facility, we have had the visit of Gerrit Kuhn, who supports PacBio in our area, and who gave a nice presentation of how … Continue reading

Posted in assembly | 1 Comment

Closing the assembly #bioinformatics

We left you with assemblies numbering tens of contigs. The next step was for our students to order them. We chose to go ahead only for strains 705 and 743. For strain 705 we had an optical map to help … Continue reading

Posted in assembly, students | 1 Comment

Progress in genome assembly: 3 strains, 6 QC parameters, 3 software, 2 k-mers #bioinformatics

Restarting this blog after a pause due to other duties, extra motivated by the acceptance of our first paper… This autumn, our students worked hard to make their millions of reads into assembled genomes. The students have worked on a … Continue reading

Posted in assembly, students | 1 Comment

Genome assembly done for two bacteria

During the Autumn semester we have sequenced and asssembled two genomes: one from a Neochlamydia and one from a Ralstonia. We have first ran one Illumina lane for both genomes, then the students assembled these reads using a variety of … Continue reading

Posted in assembly | Leave a comment