Next-generation Sequencing Analysis
Different instruments for high throughput sequencing are available at the LGTC. The generation of primary data of each of these machines, i.e. FASTQ files, are created with the software provided by the company. This includes basecalling and basic quality control assessments. Consequently the output files depend on the machine used.
In conjunction with other members of the Center for Human and Clinical Genetics we provide analysis of next-generation sequencing (NGS) data, as well as advice.
We are also active in giving the MGC course on NGS analysis. This and additional courses can also be found at our course announcements page. We also give courses, like the MGC course on NGS data analysis, Linux courses and an introduction course for using our cluster.
We have worked with data from many applications, including Exome sequencing, ChIP-seq, DeepCAGE, DeepSAGE RNA-seq, de novo sequencing, SNP, detection, and miRNA profiling. For a selection of these applications there are pipelines setup by the LGTC. However, modified or complete custom analysis are also possible.
To fit the best analysis with your experiment, we will setup an intake meeting with one of our specialists and the customer. Whenever new techniques are performed, it can be necessary to setup a custom analysis plan. Other possibilities such as annotation against a local variant database will be discussed at this point as well.
You will receive the data which can be provided via an HTTP server or external hard disks. This includes the raw data specific to the instrument used and the output files from the discussed analysis. The media and format of the files will be as what was agreed upon in the intake discussion. Whenever analysis is complete, another meeting will scheduled to review the results and conclude the project.
Software and hardware:
The software used at the LGTC will be open-source as much as possible. This means it can be freely used and distributed without any additional costs. These tools should run without any problems on any Linux based system. Our custom pipelines may require a cluster.
Regarding hardware, we can also provide services on our computer cluster for projects which need hundreds of cores or lots of memory.
If you want complete data analysis to be done it has to be included in your quotation. For questions about quotations or additional information please contact the LGTC.
Bioinformatics team from the LGTC:
For more detailed information, see our terms and conditions.