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Experience in variant calling from exome sequencing
Francesco Lescai, Elia Stupka
UCL Genomics, University College London
Sequencing whole exomes in order to identify high penetrant variants in few individuals is becoming relatively easy, and calling variants
is apparently an easy push-one-button procedure. However, understanding data quality and filtering out potential false positives in SNP calling is far more difficult. We will give a tour among the key QC and filtering issues, and discuss our experiences in calling variants from exome sequencing projects at UCL Genomics.
Analysing sequencing data on the NGS Cloud
Caroline Johnston, Matteo Turilli
The generation of large next-generation sequencing datasets is rapidly becoming a standard procedure in biology, but the resulting data requires compute resources beyond those normally available in a lab. The National Grid Service’s prototype Cloud is a first step towards a non-commercial, scalable solution for UK researchers. We will give a brief introduction to the NGS and to the Cloud prototype and will run a demo to process some short read data.
AQuA-NGS: A Quality Assessment Tool for Next Generation Sequencing Data
The recent advancement of high-throughput sequencing enables the experimentalist to generate huge amounts of data at the genomic, transcriptomic, and epigenetic levels. However, as this is a relatively new technology, the methods for assessing the quality of the data are still limited. The AQuA-NGS system was developed as a platform-independent, desktop application for the viewing of quality assessment metrics generated by the R/Bioconductor package, ShortRead. These metrics are stored in a MySQL database, together with run and sample metadata. Using the flash-based GUI, the Bioinformatician may submit new data, browse the database, view metrics via interactive tables and charts, and directly compare QA metrics across samples, on the basis of multiple criteria. The system in its present, foundational state can perform the basic functions of generating, viewing, and comparing a limited set of QA metrics generated from Illumina/Solexa export files. It requires additional development to make it ready for public release, such as the ability to process non-Solexa files, and work with remote destinations. Once complete, it will hopefully be incorporated into the pre-processing pipeline of multiple next generation sequencing platforms.
Thurs 21st October
After the talks (around 7.30 if you want to meet us there), we will be going to the Eastside Bar on Princess Gardens.