HTS training material repository


The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis.

Embarking on developing new training materials is challenging for many reasons; often trainers do not have prior experience in preparing or delivering such materials and if they do, they frequently struggle to keep them up to date.

To support trainers in materials preparation, reduce the duplication of effort by increasing the re-use of existing materials, and allow for the sharing of teaching experience among the HTS trainers community, we created a repository of curated HTS training materials.

During the “Best practices in next-generation sequencing data analysis” workshop held in Cambridge UK, in January 2015, as a consortium of 29 teachers, we have developed a strategy for materials’ curation and dissemination. This resulted in standards for describing training materials and in the establishment of the repository you are currently browsing.

The devised standards have been applied to the curation of existing materials contributed by members of the trainers' consortium. The repository has been implemented using Git, hence it is decentralized and self-managed by the community and can be forked/built-upon by all users.

This resulted in standards for describing training materials and in the establishment this repository which allows trainers to access annotated materials that can now be re-used, modified or incorporated into new courses.



What materials are available?

The repository has three main tiers: "Content", "Courses", and "Datasets", the first wrapping several modules (topics) - see the list below - regrouping lectures and materials from different contributors (authors).

RNA-Seq

RNA-Seq pipeline from initial quality control, data trimming to alignment, feature summarization and downstream differential expression analysis.

ChIP-Seq

ChIP-Seq pipeline from initial quality control, alignment, peak calling, to genomic annotation and differential binding analyses.

Variant Analysis

Variant analysis pipeline from initial quality control, to alignment, variant calling and population level analyses.

HTS Introduction

Understand sequencing technologies and common data formats.

Prerequisites

Fundamentals for working with HTS data include statistical knowledge and familiarity with a Linux envirnoment as well as programming languages such as R or Python.

Not there?

If you are missing your favorite module, get in touch with us! Looking forward to helping uploading new topics.


Get started

Download

If your goal is to re-use material - or get inspiration - for a course you are planning, start by searching and browsing the repository content online, using the 'Search the repository' and 'Visit the GitLab' repository buttons.

Not familiar with Git?

Learn about Git at Software Carpentry or try the free Git course at Code School.

Used to Git?

git clone https://microasp.upsc.se/ngs_trainers/Materials.git

Upload

If you have material you want to contribute, visit the Wiki (second button) to familiarise yourself with the annotation guidelines and then take advantage of our material annotation generator (third button).

Chat with us

Join the mailing list to stay up to date with the repository developments (low traffic)

Read the Manuscript (or cite us)

Bastian Schiffthaler et al., PLOS Computational Biology, 2016

http://dx.doi.org/10.1371/journal.pcbi.1004937


Watch tutorial videos on searching, navigating and submitting materials


Consortium Members

First NameLast NameInstitute / CompanyCountryElixir memberGoblet member
AllegraViaSapienza UniversityItalyxx
AndreasHegerMRC CGATUKxx
AndrewWarryUniversity of Nottingham (ADAC)UK  
AnnaPoetschFrancis Crick Institute/ Okinawa Institute of Science and TechnologyUK/ Japan  
AnnetteMcGrathCSIROAustralia x
AntonEnrightEMBL - EBIUK  
BastianSchiffthalerUPSC Umeå, dept. of Plant PhysiologySweden  
BertOverduinEdinburgh Genomics / The University of EdinburghUK  
BorbalaMifsudLRIUK  
CharlotteSonesonBioinformatics Core Facility, SIB Swiss Institute of BioinformaticsSwitzerlandxx
ChiaraBatiniUniversity of LeicesterUK  
DavidSimsCGAT, MRC FGU, OxfordUK  
EijaKorpelainenCSC - IT Center for ScienceFinlandxx
FrederikCoppensVIBBelgiumx 
GabriellaRusticiUniversity of CambridgeUKxx
HediPetersonUniversity of TartuEstoniax 
JennyDrnevichHPCBio & Carver Biotechnology Center, University of IllinoisUSA  
KateLeeUniversity of LeicesterUK  
LeeLarcombeELIXIR UKUK  
MarkDunningCancer Research UK, Cambridge InstituteUK  
MarkFernandesInstitute of Food ResearchUK  
MartijnHerberHanze University of Applied ScienceNL  
MartinDahlöSciLifeLabSweden  
MatthewBladesUniversity of LeicesterUK  
NicolasDelhommeUmeå Plant Science CenterSweden  
PriitAdlerUniversity of TartuEstoniax 
RadhikaKhetaniHarvard School of Public HealthUSA  
SarahMorganEMBL-EBIUKxx
SurajMenonUniversity of CambridgeUK  
TanyaDickieTGACUK