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

**URL:** <https://cwl.discourse.group/t/building-a-clinically-validated-de-novo-assembly-workflow-with-cwl-and-galaxy/262>\
**Category:** CWLcon 2021\
**Created:** [February 1, 2021, 4:40pm UTC](https://cwl.discourse.group/t/building-a-clinically-validated-de-novo-assembly-workflow-with-cwl-and-galaxy/262 "2021-02-01T16:40:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\
**Post date:** [February 1, 2021, 4:40pm UTC](https://cwl.discourse.group/t/building-a-clinically-validated-de-novo-assembly-workflow-with-cwl-and-galaxy/262/1 "2021-02-01T16:40:02Z")

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Presenter: Andrey Tovchigrechko, Kite Pharma  
Session 1 (Americas-EMEA) [Monday, February 8th 14:20 UTC](https://www.timeanddate.com/worldclock/fixedtime.html?iso=20210208T1420)

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 [https://github.com/ngs-mstb/micgent](https://www.youtube.com/redirect?v=rdyc0P198ko&event=video_description&redir_token=QUFFLUhqa0pSQkdnX2NsS2kwdFZNV3dpSHQ0MkFlVi1MQXxBQ3Jtc0tuSGhDUHRRQVZLdjZteXlZdFdNZHdxeWthcTdhbTZWVk9Ib3NDc0FaempyLVc4aHhTaFlJRy1TR0lTMENrdnRIM3NielBJLUNtSXFhMGdLWC1aXzdENFhaUjM2SHNPT0drZDdKeFFfWDNNMW1GR0F4WQ%3D%3D&q=https%3A%2F%2Fgithub.com%2Fngs-mstb%2Fmicgent) under GPLv3 license."

https://www.youtube.com/embed/rdyc0P198ko?feature=oembed&wmode=opaque&list=PLsyZRJ6E7McM_smuH9KZP-vVkPzBdVPuU&start=2

Please leave your questions for the presenter below!

As an alternative to YouTube, this presentations is also available on ConfTube

https://conf.tube/videos/embed/2a627871-1d9f-49ac-b266-24e63e32dfaa

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**Author:** ![nsoranzo](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/nsoranzo/32/163_2.png) [@nsoranzo](https://cwl.discourse.group/u/nsoranzo)\
**Post date:** [February 11, 2021, 4:27pm UTC](https://cwl.discourse.group/t/building-a-clinically-validated-de-novo-assembly-workflow-with-cwl-and-galaxy/262/2 "2021-02-11T16:27:52Z")

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