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PRBB Computational Genomics Seminars Luca Cozzuto

PRBB Computational Genomics Seminars Luca CozzutoPRBB Computational Genomics Seminars Luca Cozzuto

23/06/2022
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PRBB Computational Genomics Seminars Luca Cozzuto

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23/06/202212:00OnlinePRBB Computational Genomics SeminarsLuca CozzutoBioinformatics Unit (Julia Ponomarenko), CRGAnalysis of nanopore data using Master of Pores 2Host: Garrido Enamorado, RominaAbstract:Link: https://us02web.zoom.us/j/84212222322?pwd=VmVIdHo3czlFcVZUSDhscnQ0RzN5Zz09
Abstract:
Master Of Pores2 (MoP2) is a suite of Nextflow-based pipelines for fully reproducible processing and analysis of the Nanopore sequencing data, both cDNA and RNA, with a focus on in-depth analysis of direct RNA-seq data. The first module of the software is for pre-processing raw fast5 files applying base calling (using either CPU or GPU) and read demultiplexing, filtering, aligning and assembling, producing a comprehensive report. The second module is used for predicting modified RNA bases applying four different approaches that can be chosen independently. The third module was developed for estimating the length of polyA tails using two independent approaches. The fourth module implement a method for improving the predictions made by the second module generating a consensus with fewer false positives. MoP2 is implemented using the new Nextflow DSL2 syntax, it is completely modular and scalable up to the amount of data produced by a PromethION flowcell. For small datasets, the integrated pipelines can be run on a laptop, and, for large datasets, in different HPC or cloud environments.