Linelle Abueg - Reproducible & high-quality genome assembly on public computational infrastructure скачать в хорошем качестве

Linelle Abueg - Reproducible & high-quality genome assembly on public computational infrastructure

Recent improvements in genome sequencing and assembly have facilitated the possibility of generating high-quality reference genomes for all species; however, the process of genome assembly is still computationally intensive, requires significant expertise, and is difficult to scale up for multi-species efforts. To address these barriers for entry into genome assembly, the Vertebrate Genomes Project (VGP) has made their assembly pipeline freely available on the public computational infrastructure Galaxy. This enables researchers to use the pipeline on their data without requiring local computational resources or programming expertise. The VGP has also made several training modules available on Galaxy’s robust training and tutorial network, to help guide newcomers on how to use the pipeline. The pipeline has been substantially improved from earlier versions by integrating PacBio HiFi long reads and Hi-C based phasing during assembly, before further scaffolding with Bionano and/or Hi-C data. The pipeline is implemented as modular workflows, so that individual researchers can adapt it to their specific data availability. Quality control metrics are automatically generated and reported throughout the pipeline, simplifying the process for the end user. We have successfully used the pipeline on large and small genomes from a variety of taxonomic groups, both vertebrates (birds, fishes, reptiles, and mammals, including humans) and invertebrates. Here we report on how to use the pipeline and how the current version of the pipeline generates significantly better assemblies than previous ones. We anticipate that the availability of this pipeline will be instrumental to the success of large-scale genomics projects, and for democratizing the process of genome assembly in general.