bcbio-nextgen.readthedocs.io
Teaching — bcbio-nextgen 1.0.2 documentation
http://bcbio-nextgen.readthedocs.io/en/latest/contents/teaching.html
Common Workflow Language (CWL). This is a teaching orientated example of using bcbio from the Cold Spring Harbor Laboratory’s Advanced Sequencing Technology and Applications course. This uses cancer tumor normal data from the ICGC-TCGA DREAM synthetic 3 challenge. Subset to exomes on chromosome 6 to reduce runtimes. It demonstrates:. Running a cancer tumor/normal workflow through bcbio. Analysis with human genome build 38. SNP and indel detection, with 3 variant callers and an ensemble method. The exampl...
docm.genome.wustl.edu
DoCM - Database of Curated Mutations
http://docm.genome.wustl.edu/news
Major website update. A new importing system. Was implemented to facilitate batch imports. This streamlines the import process and is documented in the batch submission help. Page The database was reorganized in to batches and reprocessed through the new automated importer. Database update. Kin-driver. And pan-cancer recurrent hotspots. Variants were added to DoCM. Database update. Automatic importer implemented to automatically import relevant variants from CIViC. DoCM cited by Krogan, N. J., Li...DoCM ...
bcbio-nextgen.readthedocs.io
Configuration — bcbio-nextgen 1.0.2 documentation
http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html
Multiple files per sample. Sample or run specific resources. Common Workflow Language (CWL). Two configuration files, in easy to write YAML format. Specify details about your system and samples to run:. High level information about the system, including locations of installed programs like GATK and cores and memory usage (see Tuning core and memory usage. Details about a set of samples to process, including input files and analysis options. You configure these for each set of samples to process. Input, w...
docm.genome.wustl.edu
DoCM - Database of Curated Mutations
http://docm.genome.wustl.edu/faq
FAQ Frequently Asked Questions. How do I cite DoCM? A manuscript for DoCM is currently in preparation. In the meantime please cite http:/ docm.genome.wustl.edu. How do I contribute a variant to DoCM? We welcome candidate variant submissions which will allow this resource to be more comprehensive and useful to the community at large. If you have a submission please fill out a variant submission form. If you would like to contribute your curation efforts to DoCM please contact us. How do I use the DoCM API?
smallchangebio.wordpress.com
Notes: Bioinformatics Open Source Conference 2015 day 2 afternoon: Translational, Visualization and Lightning Talks | Small Change Bioinformatics
https://smallchangebio.wordpress.com/2015/07/11/bosc2015day2b
Notes: Bioinformatics Open Source Conference 2015 day 2 morning — Ewan Birney, Open Science and Reproducibility. Notes: Bio in Docker Symposium 2015 day 1: ngs pipelines, workflow tools, volume management →. July 11, 2015. Notes: Bioinformatics Open Source Conference 2015 day 2 afternoon: Translational, Visualization and Lightning Talks. I’m at the 2015 Bioinformatics Open Source Conference (BOSC). My other notes from the conference:. Holly Bik and Data Science. Tobias talks about work on defining action...
onco-seq.e-cancer.fr
Onco-Seq: Onco-Seq du 17 novembre
http://onco-seq.e-cancer.fr/2016/11/onco-seq-du-17-novembre.html
Ce bulletin de l'Institut National du Cancer s'intéresse à l'actualité des techniques de séquençage du génome et à leurs applications. La publication des billets se fait sur un rythme hebdomadaire. Jeudi 17 novembre 2016. Onco-Seq du 17 novembre. Bioinformatique and Big Data. Ilumina ont dévoilé leurs projets de collaboration sur plusieurs logiciels de la suite. Voir aussi le communiqué. Pour comprendre comment les tumeurs développent une résistance aux traitements (voir aussi Genome Web. A procédé au la...