40 HIGHLIGHTED PUBLICATION GENOMICS In 2022, the Novaseq Illumina sequencer is the primary machine for short read sequencing, having replaced the NextSeq platform which has been laid off. The number of sequencing hours on the Novaseq has increased significantly from 600h in 2019 to 2500h in 2022, resulting in faster turnaround times and lower sequencing costs. This was made possible through the acquisition of the Novaseq Illumina sequencer in 2019, which was supported by FEDER grants. The platform has acquired a third MiSeq Illumina sequencer, which is particularly useful for amplicon sequencing with read lengths of up to 500bp. Despite the introduction of newer machines, the MiSeq remains the best option for this type of sequencing. The platform has upgraded from the Agilent Bioanalyser to the more versatile Agilent Fragment Analyser (FA), which is used to quality control DNA and RNA samples received from users of its sequencing services. The FA has a much broader resolution range of fragments up to 60kb in length, making it compatible with long read sequencing, and is much more automated, with the ability to handle 96-well plates. In collaboration with the CHU the Genomics Platform has now access to a GridION and a P2 solo from Oxford Nanopore. The GridION can run and analyze up to five MinION flowcells simultaneously, while the P2 solo is compatible with PromethION flow cells, with the capacity to sequence a human genome at 30X coverage using long reads. BIOINFORMATICS In 2022, the Bioinformatics Platform became independent and starteddeveloping its own activities. Theplatformconsolidated its role of support for the community by performing more than 65 analyses of bulk and single-cell RNAseq data distributed between 18 GIGA teams, 4 Veterinary Faculty’s teams and 4 biotechs. The Bioinformatics Platform has also started organizing trainings on programming languages and on analysis modules. The first session of courses has been followed by more than 30 GIGA members from 10 URTs. Consolidating its collaboration with the genomics platform, the team has implemented a pipeline to accelerate the demultiplexing of data coming out of Illumina sequencers and a robust pipeline to analyse RNAseq data generated on both Illumina (short reads) and Nanopore (long reads) sequencers. The team has also developed a graphical interface to visualize genotyping data and adapt quality filtering thresholds. As more and more teams are performing single-cell RNAseq experiments, the GIGA-bioinformatics team has started to develop a pipeline to perform these analyses, including the analysis of cell velocity and the identification of cell populations. This pipeline will include a user-friendly graphical interface allowing the exploration of the analysis results and the generation of figures for publication. End of 2022, a total of 1078 users had used the mass storage, occupying 1340 Tb of disk space for a total of 274 million files. Moreover, in 2022, GIGA members and collaborators have run more than 6 million jobs on the GIGA High Performance Computing Cluster, for a cumulated calculation time (CPU time) of 2 million hours. Beside the support to these users, the Bioinformatics Platforms has also obtained funds from the University (CURV) to increase the storage capacity of the mass storage and of the cluster. Those will be installed in 2023. PLATFORMS HIGHLIGHTS
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