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    Next-Generation Sequencing Workshop 2017

    Genome Assembly & Variant Calling

    Workshop Purpose

    This 2-days training workshop has two main goals. The first goal is to introduce scientists to NGS, teach them how to use it as part of their research and help them to select the appropriate sequencing technology.

    The second goal is to introduce scientists to NGS analysis through a set of detailed practical exercises on real data to perform genome assembly and variant calling. Check out the detailed workshop program here.

    The workshop will be presented by Dr. Layal Yasin, a bioinformatician and founder of Bioinformatics Experts.

    Skills You Will Gain

    Genome Assembly

    You will be able to assemble genomes out of reads produced by NGS. The assembly will either be done by mapping the reads to a reference genome, or by reconstructing the genome from overlapping reads without using a reference genome.

    Variant Calling

    This workshop will introduce you to the needed tools to perform variant calling. You will perform this by yourself using real data.

    Computer Skills

    You will learn how to use your own computer to use NGS analysis tools. Moreover, you will learn how to use bash by applying basic commands.

    Target Audience

    Researchers in the biology and medical domain and related fields. The audience is expected to have little to no experience in next-generation sequencing analysis.

    Available seats: 30


    Attendees are expected to have knowledge in molecular biology. Linux or mac laptop is required. For windows users, please install a linux partition on your laptop. Don’t know how to do it? contact us at and we will assist you in this.

    Workshop Program

    Morning Session: 9:00 – 11:00

    Introduction to next-generation sequencing

    Sequencing Instruments

    Sequencing techniques


    Coffee Break; 11:00 – 11:30


    Mid-day Session: 11:30 – 13:30

    Output of sequencing instruments

    Understanding data formats (fasta, fastq)

    Processing raw reads: quality check and reads trimming using fastqc

    Introduction to bash shell


    Lunch Break: 13:30 – 14:30


    Afternoon Session: 14:30 – 16:00

    Introduction to genome assembly: mapping to a reference genome

    Read mapping using bwa aligner

    Understanding mapping output (SAM/BAM format)

    Morning Session: 9:00 – 11:00

    Introduction to genome assembly: de novo assembly

    Learning how to assemble de novo genome

    Visualising the assembly


    Coffee Break: 11:00 – 11:30


    Mid-day Session: 11:30 – 13:30

    Introduction to variant calling

    Installing and using bcftools  to call variants

    Understanding variant calling output (VCF files)

    Visualising SNPs graphically


    Lunch Break: 13:30 – 14:30


    Afternoon Session: 14:30 – 16:00

    Open discussion

    Register for the workshop

    Registration and attendance are free of charge.

    Workshop Venue & Date



    starting at 9:00

    For additional information, please contact us at