NGI and NBIS webinar on de novo sequencing and analysis
May 26 @ 10:00 – 12:00 CEST
Welcome to a webinar on de novo sequencing and analysis, a service that the National Genomics Infrastructure (NGI) and National Bioinformatics Infrastructure Sweden (NBIS) offers to its users. De novo, which translates to “starting from the beginning”, refers to the process of sequencing a novel genome from an organism where no previous reference sequence is available.
The de novo analysis strategy is divided into separate stages, starting with
(i) sequencing,
(ii) assembly, and finally
(iii) annotation.
During the sequencing stage, short and/or long DNA/RNA reads are produced using several sequencing technologies, such as Illumina, PacBio and Nanopore. The obtained DNA reads are subsequently assembled into longer sequences, called contigs during the assembly stage. The gaps between contigs can be linked by scaffolding using long read data and chromosome contact maps obtained by Hi-C.Assembled genomes are then annotated, allowing for the structure and the function of the assembled sequences to be inferred. This includes protein-coding genes, but also other features such as non-coding genes and regulatory elements. This webinar will focus on what one needs to consider while planning a de novo project. We are also proud to have Alexander Suh (Lecturer, University of East Anglia and Uppsala University) describing one of his many projects on how to solve sex-specific and tissue-specific genome differences of birds by using de novo tools facilitated by NGI and NBIS.
Agenda
| 10:00 | De novo analysis that NGI can offer you Olga Vinnere Pettersson, PhD, Project coordinator NGI |
| 10:20 | PacBio/Nanopore in de novo realm Ignas Bunikis, PhD, Bioinformatician NGI |
| 10:35 | Using Hi-C methods to generate chromosome-scaled assembly scaffolds Remi-Andre Olsen, PhD, Bioinformatician NGI |
| 10:50 | The assembly and annotation support available at the SciLifeLab bioinformatics platform NBIS Henrik Lantz, PhD, Joint Head of Unit Support and Infrastructure NBIS |
| 11:05 | Diving into the depths of sex-specific and tissue-specific genome differences of birds Alexander Suh, PhD, Lecturer, University of East Anglia and Uppsala University |
| 11:30 | Q&A session |
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