Biodiversity Genomics Europe and SciLifeLab HiC Course
August 29, 2025 · View on GitHub
This repository contains the digitized versions of all course streams for the 'Biodiversity Genomics Europe and SciLifeLab HiC Course'.
Description
| Title | Biodiversity Genomics Europe and SciLifeLab Hi-C Course |
| Description | A course aiming to provide open, sustainable training in laboratory preparation of Hi-C libraries for reference genome sequencing of non-model organisms for BGE partner sequencing centers. |
| Type | Video |
| Language | English |
| Keywords | Hi-C, genomics, biodiversity, sequencing |
| Authors | Maria Laura Aguilera Gil4  , Lorenzo Ballini8 , Laurie Bertrand3 , Simona Buonanno7 , Eunkyong Choi6 , Annunziata De Luisi7, Giada Ferrari9 , Leonardo Girlanda8 , Carmela Gissi7 , Maria Gyftea6 , Brian Kilburn1, Karine Labadie3 , Tuuli Lundback-Lärva6 , Graeme Oatley5 , Fernando Cruz Rodriguez4 , Irene Fabiola Roman Maldonado5 , Lily Shiue2 , Morten Skage9 , Pamela Veneziano Broccia4 , Ave Tooming-Klunderud9 , Olga Vinnere Pettersson6 1 Arima Genomics (US) 2 Cantata Bio (UK) 3 Genoscope (FR) 4 National Center for Genomic Analysis (ES) 5 Sanger Institute (UK) 6 SciLifeLab (SE) 7 University of Bari Aldo Moro (IT) 8 University of Florence (IT) 9 University of Oslo (NO) |
| Author contact details | olga.pettersson@igp.uu.se |
| Content Provider | SciLifeLab and Biodiversity Genomics Europe consortium |
| Contributors | Kristen Schroeder1 , Jill Jaworski1 , Hampus Pehrsson Ternström1 1 SciLifeLab (SE) |
| Date created | June 9-14, 2024 |
| Date published | August 31, 2025 |
Accessibility
| URL | BGE and SciLifeLab HiC Course |
| DOI | course repository: https://doi.org/10.5281/zenodo.14643653 Introductory Course Stream archive: https://doi.org/10.5281/zenodo.16811295 Challenging Samples Course Stream archive: https://doi.org/10.5281/zenodo.16812209 AssemblyLink Course Stream archive: https://doi.org/10.5281/zenodo.16926087 |
| Access costs | No |
| Events | None |
Educational
| Learning outcomes | By the end of the course, participants will be able to: - independently prepare HiC libraries of low-complexity samples. - prepare HiC libraries at their home labs. - understand the most crucial steps of the protocol - troubleshoot crucial steps of the protocol in their home labs when applied to high-complexity samples |
| Structure and duration | Introductory stream - 2h40m video content Challenging Sample stream - 3h20m video content AssemblyLink stream - 2h30m video content Discussion content - 3h15m video content |
| Target audience | Researchers with an interest in starting or continuing with Hi-C technique for non-model organisms in their research. Course streams include introductory, intermediate, and advanced levels. |
| Expertise (skill) level | Intermediate/Advanced. This course is intended for an audience familiar with labwork and research best practices. |
| Prerequisite - knowledge | Participants must have: - an understanding of fundamental genomics and epigenomics concepts - the ability to demonstrate basic laboratory technique, including safe laboratory practices. Participants should have: - an understanding of their local permit and safety requirements for processing and handling samples and reagents for HiC. |
| Additional information | Arima Genomics Arima High Coverage HiC Kit User Guide for Animal Tissues (Document Part Number A160162 v01) Dovetail AssemblyLink Kit User Guide (Version 1.0 May 30, 2024). |
Reuse
| Licensing and reuse details | The Arima HiC protocol used in this course is © 2019, Arima Genomics, Inc. All rights reserved. The AssemblyLink protocol used in this course is © 2024, Cantata Bio, LLC. All rights reserved. The video materials from this course are available for reuse under  |
| Preferred citation | For citation of the entire course material, please use: Maria Laura Aguilera Gil, Lorenzo Ballini, Laurie Bertrand, Simona Buonanno, Eunkyong Choi, Annunziata De Luisi, Giada Ferrari, Leonardo Girlanda, Carmela Gissi, Maria Gyftea, Brian Kilburn, Karine Labadie, Tuuli Lundback-Lärva, Graeme Oatley, Fernando Cruz Rodriguez, Irene Fabiola Roman Maldonado, Lily Shiue, Morten Skage, Pamela Veneziano Broccia, Ave Tooming-Klunderud, Olga Vinnere Pettersson (2025). Biodiversity Genomics Europe and SciLifeLab HiC Course. DOI:10.5281/zenodo.14643653. |
| Status | under development |
| Version | v.1-full |
| Date of last revision | August 31, 2025 |
| Modification contact person | traininghub@scilifelab.se |