Course Overview: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

    Course Overview/description: 

    Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential informatics skills required to begin analysing NGS data and apply some of the most commonly used tools and resources for sequence data analysis.

    The programme will cover prominent sequencing technologies, algorithmic theory and principles of bioinformatics, with a strong focus on practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis - QC, alignment, assembly, variant calling and RNA-Seq.

    This course will apply a blended learning format consisting of locally coordinated classrooms referred to as “remote classrooms”. Click here for more information. Please note: Due to the COVID-19 pandemic, the local classrooms will likely run virtually, using Zoom and downloadable virtual machines. 

    Intended Audience:

    Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving next generation sequencing data analysis.

    Priority will be given to applicants who 1) currently or will soon have NGS experimental data to analyse 2) will utilise the bioinformatics techniques taught in at least two of the modules/topic areas listed in the programme outline in their experiments 3) have a clear plan/opportunity to disseminate the knowledge amongst their peers. We encourage applicants to highlight these areas in their application.

    Learning objectives/outcomes: After this workshop participants should be able to:

    • Use the unix command-line as a tool for data analysis
    • Describe the different NGS data file formats available
    • Perform QC assessment of high throughput sequencing data
    • Explain the algorithmic concepts behind read alignment, variant calling and structural variant detection
    • Perform read alignment, variant calling and structural variation detection using standard tools
    • Analyse RNA-Seq and CHiP-seq data
    • Perform a genome assembly using NGS data 


    The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous experience using the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

    Syllabus and Tools:

    The course will cover the following topics:

    • Intro to Unix/Linux & running workflows
    • Introduction to NGS Technologies
    • NGS data pre-processing and QC
    • Alignment to reference sequences
    • Variant calling and annotation
    • ChipSeq
    • RNASeq
    • Genome assembly

    Dates for the workshop:

    Tuesdays & Thursdays from 22/03/2022 until 20/06/2022 (staff training will happen ahead of this)

    Classroom registration opens:


    Classroom registration closes:


    Notification date:



    Workshop organisers:

    WGC WCS and H3ABioNet

    Workshop Sponsors:

    Wellcome Genome Campus/ Wellcome Connecting Science and H3ABioNet 


    NGS, Data analysis, Genomics, Sequence analysis

    Skill level of training:




    Credential awarded:

    Letter of completion

    Type of training:

    Likely to be run in a virtual format

    Workshop limitations:

    The course aims to provide a hands-on introduction to bioinformatics for next generation sequencing, and should not be considered a complete education in the theoretical and mathematical foundations of the topics.

    Workshop Programme:

    The workshop will run for ~10 weeks, on Tuesdays and Thursdays from the 22nd of March until the 20th of June. 


    Please apply to take the course by clicking here


    , ,


    Page 3 of 4

    © 2021
    Terms - Privacy - Policy & Safety - Helpdesk
    The H3ABioNet website content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health