Difference between revisions of "Bioinformatic pipeline"
Farmakorakel (talk | contribs) (Created page with "==Outline== * Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow] * Packaging the pharmacogenomic varian...") |
Farmakorakel (talk | contribs) (→Outline) |
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==Outline== | ==Outline== | ||
* Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow] | * Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using [https://www.nextflow.io/ Nextflow] | ||
| − | * Packaging the pharmacogenomic variant callers in a [https://www.sylabs.io/docs/ Singularity container] for increased portability | + | * Packaging the pharmacogenomic variant callers in a [https://www.sylabs.io/docs/ Singularity container] for increased portability (the [[Pharmacotyper]]) |
** Using [https://github.com/inumanag/aldy Aldy] for genotyping of genes for absorption, distribution, metabolism, and excretion (ADME). | ** Using [https://github.com/inumanag/aldy Aldy] for genotyping of genes for absorption, distribution, metabolism, and excretion (ADME). | ||
** Using [https://github.com/humanlongevity/HLA xHLA] for genotyping of the HLA-gene. | ** Using [https://github.com/humanlongevity/HLA xHLA] for genotyping of the HLA-gene. | ||
* Making test for continuous integration of pharmacogenomic variant calling in the pipeline | * Making test for continuous integration of pharmacogenomic variant calling in the pipeline | ||
** Verified test data sets for Aldy are [https://github.com/inumanag/aldy-paper-resources publicly available] | ** Verified test data sets for Aldy are [https://github.com/inumanag/aldy-paper-resources publicly available] | ||
Latest revision as of 10:30, 27 February 2019
Outline
- Integrate pharmacogenomic variant calling in the hospital bioinformatic workflow using Nextflow
- Packaging the pharmacogenomic variant callers in a Singularity container for increased portability (the Pharmacotyper)
- Making test for continuous integration of pharmacogenomic variant calling in the pipeline
- Verified test data sets for Aldy are publicly available
