Transcriptome assembly – Bioinformatics workshop

Assembly of the transcriptome based on data from Next-Generation mRNA sequencing (RNAseq) is a powerful tool for detecting changes in gene expression. Allows comparison of conditions, tissues or strains / species. However, the ability to accurately perform such comparative analyzes is fundamentally dependent on the quality of the assembly. In particular for the detection of sequence variants, but also for the detection of isoforms and quantification of transcripts, incorrect gene assembly can significantly skew the results. These problems are particularly pronounced in non-model organisms in the absence of a suitable reference genome, where RNA-Seq is used to reconstruct and quantify whole transcripts.

At first glance, the process of assembling a transcriptome appears to be similar to assembling the genome, but in reality there are fundamental differences and different challenges. These include different levels of gene expression, where errors in analytical tools can, for example, lead to misinterpretation of this low level of gene expression as sequencing errors, presence of isoforms due to alternative splicing, repetition, etc. The assembly problem is complicated by the transcriptome differing between different cell types, environmental conditions and time points. Successfully performing transcriptome assembly means taking all these aspects into account.

Our workshop is focused on bioinformatics processing of RNA-Seq data and transcriptome assembly. We will guide you through data quality control, filtering, efficient and accurate correction of sequencing errors, assembly of the transcriptome and its evaluation.


What will you learn?

  • How to select and use the most appropriate procedure for editing RNA-seq data and their assembly
  • How to process data from raw data (reads) to their assembly into the target transcriptome
  • How to evaluate the results 
  • You will gain your own experience with a wide range of bioinformatics tools focused on the analysis of NGS data
  • You will have the opportunity to communicate with an experienced team of speakers and other participants


Who should attend?

  • The event is intended for advanced applicants, biologists or bioinformaticians interested in this specific area of data analysis.
  • Knowledge of BASH and the terminal is a prerequisite. If you have no experience with the analysis of sequencing data, we recommend that you first complete the more general Next-Generation Sequencing data analysis – Workshop for beginners to learn the basics.
  • If in doubt, do not hesitate to contact us.




  • Quality control of sequencing reads
  • Read repair
  • Trimmming of adapter and low quality bases from fastq files
  • Removal of remaining over-represented and unwanted sequences (rRNA reads)
  • Transcriptome assembly
  • Assessing assembly quality
    • Basic alignment summary metrics
    • How to quantify read support for the assembly
    • How to quantify completeness (BUSCO)




  • The team of lecturers is composed of professionals, employees of SEQme and possibly invited guests - experts on the topic, who have long been using various Next-Generation sequencing technologies. They focus not only on data analysis, but also on laboratory processing of samples in the NGS laboratory, design of NGS projects and other related tasks and are therefore able to provide a comprehensive insight into the whole issue in context.
  • SEQme is not an official distributor of any NGS technology company (Illumina, IonTorrent, PacBio, OxfordNanopore, etc.). We are users, just like you. In our sequencing laboratories, we always use the most suitable technologies from various manufacturers, always with the aim of maximum effect for your sequencing projects. We then share the knowledge gained in this way with the participants of our courses and workshops.


Event details:

  • Trainers always explain the topics using presentations, but the main emphasis is on subsequent practical demonstrations so that all participants actively learn to use the explained procedures and tools
  • All participants themselves perform important steps of NGS data analysis, each has their own computer!
  • We use powerful computers, which are provided to all participants of the event. Using your own computers and / or data files is not possible.
  • If it is an online workshop, you will need your own computer with an Internet connection - you will remotely connect to our powerful analytical computers. There are no special demands on your computer, it is important to have admin rights to install one or two software packages to enable the connection. Simple instructions on how to connect to our workstations will be provided to registered participants well in advance of the event. We recommend that you have headphones to communicate with our lecturers and consider having two monitors - sometimes it is necessary to have multiple windows open at once and having two monitors is comfortable.


Event logistics:

  • Language: English
  • The registration fee includes printed presentations for the course / workshop (for online events, presentations are provided exclusively in electronic form). If this is the „physical“ event (i.e. this is not an online workshop), the price also includes lunches and refreshments.
  • Lodging, travel and other incidental expenses are the responsibility of the attendee.
  • Please note that no laboratory experiments are performed during the event.


Special offer:

All our courses and workshops can also be organized at your workplace, for your working group. So as a tailor-made event. Some of our events were even created in this way - at the client's request. The advantage of this format is, of course, the ability to prepare a turnkey event for your team, reflect your specific requirements and needs, including the ability to work with your data. If you are interested, do not hesitate to contact us.

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