Building a Clinically Validated De-novo Assembly Workflow with CWL and Galaxy

Presenter: Andrey Tovchigrechko, Kite Pharma
Session 1 (Americas-EMEA) Monday, February 8th 14:20 UTC

Summary: “ NGS-MSTB is a pipeline for assembling next generation sequencing reads from large scale viral and bacterial clinical strain surveillance studies to monitor potential drug resistance and the presence of virulence factors. Using the pipeline’s integrated graphical interface, an analyst can routinely assemble and review thousands of datasets in one batch within a few hours on a compute cluster. The software assembles de-novo complete viral genomes from amplicon-derived shotgun reads potentially sequenced with extremely high local coverage variability as well as specific bacterial genes from whole genome shotgun reads. The software was successfully deployed as the assembly module in a system validated according to good clinical practices (GCP). To this end, it guarantees deterministic results, full provenance data and ensures the integrity of the inputs and intermediate datasets through cryptographic checksums. Source code, testing datasets and a Docker image are freely available at under GPLv3 license."

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Galaxy workflows are definitely composable! A workflow can in fact be used as a step inside another workflow.

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