NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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PromethION secondary analysis

Additional compute intensive nanopore raw data processing services provided by NGI

As a standard, raw nanopore sequencing data is basecalled using the latest version of production basecaller provided by Oxford Nanopore Technologies. However, developments and improvements in the field of base accuracy are very rapid. New versions of basecallers are released to community for testing and evaluation purposes, often providing significant improvements to base quality. Eventually all new features are implemented into production version of basecaller.

In some cases it might be highly beneficial to utilize newest improvements in Oxford Nanopore base calling software. Therefore many researcher choose to rebasecall their raw nanopore data. This is usually not a problem if the data sets are relatively small. But can become a challenge if one has several large data sets generated using, for example, PrometION sequencer. Basecalling is computationally intensive process, highly dependent on availability of graphic accelerators and require substantial amount of fast storage.

Therefore NGI offers rebasecalling (with possibility to utilize latest basecalling model trained to identify base modifications) as additional on demand service. Please contact long-read project coordinators for more information regarding this service.

Applications
Method Status

Service

We are routinely running this method. Please visit the Order Portal to place an order.

Keywords
Compatible Methods