<section data-background-image="https://maxulysse.github.io/assets/img/background/Sarek-Park-02.jpg" data-background-opacity=0.5 > [](https://nf-co.re/sarek) <!-- .element class="image-H10" --> ## a workflow to detect germline and somatic mutations in WGS/WES <small> Maxime Garcia / [<i class="fab fa-twitter"></i> @gau](https://twitter.com/gau) / [<i class="fab fa-github"></i> @MaxUlysse](https://github.com/MaxUlysse) [<i class="fa fa-globe-europe"></i> maxulysse.github.io/vcbs2020](https://maxulysse.github.io/vcbs2020) [The Swedish Childhood Tumor Biobank](https://ki.se/forskning/barntumorbanken) / [National Genomics Infrastructure](https://ngisweden.scilifelab.se/) [Victorian Cancer Bioinformatics Symposium 2020](http://viccancerbioinfsymposium.org/), Victoria, Australia [virtual] - 2020/10/28 </small> --- [](https://www.nextflow.io/) <!-- .element class="image-50" --> * Workflow manager * Data driven language * Portable * executable on multiple platforms * Shareable and reproducible * with containers or virtual environments * `Docker`, `Singularity` or `conda` --- [](https://nf-co.re/sarek) <!-- .element class="image-H10" --> * Open-Source [Nextflow](https://www.nextflow.io/) Pipeline * Started at [SciLifeLab](https://scilifelab.se/) * [National Genomics Infrastructure](https://ngisweden.scilifelab.se/) * [National Bioinformatics Infrastructure Sweden](https://www.nbis.se/) * Support from [The Swedish Childhood Tumor Biobank](https://ki.se/forskning/barntumorbanken) * Part of the [nf-core](https://nf-core) community * Support from [QBiC](https://qbic.life) --- ## Workflow [](https://github.com/nf-core/sarek/releases/tag/2.6.1) <!-- .element class="image-25" --> --- ## Try it now [Quick start guide](https://nf-co.re/sarek/dev#quick-start) On your own computer with test data: ```bash curl -s https://get.nextflow.io | bash nextflow run nf-core/sarek -r 2.6.1 -profile docker,test ``` Start your own analysis: ```bash nextflow run nf-core/sarek -r 2.6.1 -profile docker --input sample.tsv --genome GRCh38 ``` --- ## What is coming soon * DSL 2 ([dsl2](https://github.com/nf-core/sarek/tree/dsl2)) with [@ggabernet](https://github.com/ggabernet) and [@FriederikeHanssen](https://github.com/FriederikeHanssen) * Validation tests * More tools * Sub-workflows for specific usage * Improved cloud usage * Improved usage for non-model organism * Joint Variant Calling * More downstream processing of the final vcf files --- ## Publication in F1000Research Sarek: A portable workflow for whole-genome sequencing</br> analysis of germline and somatic variants</br> [version 2; peer review: 2 approved] <small> Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin,</br> Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz De Ståhl,</br> Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt </small> [<i class="ai ai-doi"></i> doi.org/10.12688/f1000research.16665.2](https://doi.org/10.12688/f1000research.16665.2) --- ## Get involved * Our code is hosted on Github * [<i class="fab fa-github"></i> github.com/nf-core](https://github.com/nf-core) * [<i class="fab fa-github"></i> github.com/nf-core/sarek](https://github.com/nf-core/sarek) * We have slack * [<i class="fab fa-slack"></i> nfcore.slack.com](https://nfcore.slack.com/) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/sarek](https://nfcore.slack.com/channels/sarek) --- <div class="r-stack"> <img src="/assets/img/svg/acknowledgments_2020.svg" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-out" data-fragment-index="0"/> <a href="https://nf-co.re/community#organisations"> <img src="/assets/img/svg/institutes_2020.svg" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="0"/></a> <a href="https://nf-co.re/community#contributors"> <img src="/assets/img/slides/nf-core_contributors_jobim.png" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="1"/></a> <a href="https://nf-co.re/sarek/stats#contributors"> <img src="/assets/img/slides/nf-core_sarek_contributors_2.6.1.png" title="Acknowledgements" alt="Acknowledgements" class="image-75 fragment fade-in-then-out" data-fragment-index="2"/></a> </div> --- <section data-background-image="https://maxulysse.github.io/assets/img/background/Stockholm-by-night.jpg" data-background-opacity=0.5 > ## Any questions * [<i class="fa fa-globe-europe"></i> nf-co.re](https://nf-co.re) * [<i class="fab fa-github"></i> github.com/nf-core](https://github.com/nf-core) * [<i class="fa fa-globe-europe"></i> nf-co.re/sarek](https://nf-co.re/sarek) * [<i class="fab fa-github"></i> github.com/nf-core/sarek](https://github.com/nf-core/sarek) * [<i class="fab fa-slack"></i> nfcore.slack.com/channels/sarek](https://nfcore.slack.com/channels/sarek)