Create 2016_08_01_genomics_standards.md

Author: Rachel Shekar

meeting-notes/2016_08_01_genomics_standards.md

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+---
+layout: post
+title: "August 2016 Genomic Standards Committee Meeting Notes"
+modified:
+categories: blog
+excerpt:
+tags: []
+image:
+  feature:
+date: 2016-08-01T20:43:38-05:00
+---
+
+#
+# TERRA Ref Genomics Standards Committee Meeting
+
+## **Participants**
+
+David LeBauer, Christine Laney, Michael Gore, Carolyn Lawrence-Dill, Eric Lyons, Noah Fahlgren
+
+REGRETS:
+Todd Mockler, Max Burnette, David Lee, Geoff Morris, Craig Willis
+
+## **Agenda**
+
+Introductions
+
+Objective: review current status of pipeline and plans for first data release in November.
+
+Overview (Noah)
+
+Sequencing
+
+- what has been done
+  - 192 resequenced genomes (~20-30x coverage each) from Steve K. bioenergy assoc. panel (BAP)
+  - 192 additional samples sent to HudsonAlpha one week ago (20-30x)
+  - External funding
+    - Illumina for additional ~1000 sequences
+    - DOE CSP for de novo
+  - Data quality control and analysis to date done on the Danforth Center cluster
+    - Trimmomatic => bwa => GATK => CNVator
+    - By November: user will upload raw sequencing data and metadata to TERRAref pipeline using CoGe (below)
+- what is in pipeline
+  - Raw data and experimental metadata added to Clowder
+  - Clowder extractor
+    - Upload data to the CyVerse data store (TERRA-REF)
+    - Launch CoGe workflow using the API
+  - Synchronize results back to Clowder/BETYdb
+
+- Clowder: a database that can hold data of any format. Data being imported to clowder will automatically trip extractor that will move data to the correct location for discovery and analysis
+- Data will be uploaded to NCBI, SRA
+  - Can we link from the SRA to CyVerse and Clowder easily and robustly?
+
+CoGe pipeline
+
+- A sample analysis: [https://genomevolution.org/coge/NotebookView.pl?nid=1344](https://genomevolution.org/coge/NotebookView.pl?nid=1344)
+- Draft implementation: [https://github.com/terraref/computing-pipeline/blob/f94a87f851b37ff74ded5b7b6b3b0c1e13107720/scripts/coge/coge\_upload.json](https://github.com/terraref/computing-pipeline/blob/f94a87f851b37ff74ded5b7b6b3b0c1e13107720/scripts/coge/coge_upload.json)
+
+Downstream Analyses
+
+- GOBII
+- Other downstream tools?
+  - SNP callling via CoGe
+  - What is already within CoGe
+  - Putting proprietary GATK on CyVerse (Mike G will send more info)
+  
+Data Sharing
+
+- when, where, and with what will we share as of November
+- Currently using CyVerse data store ( [https://de.iplantcollaborative.org/de/](https://de.iplantcollaborative.org/de/))
+  - [terraref/reference-data/19](https://github.com/terraref/reference-data/issues/19)
+- Phytozome  (a DOE database)- is this an appropriate for our data? Perhaps not for raw reads (Mike G)
+  - Maybe we can submit variation information from the CoGe pipeline and update it as the reference genome is updated
+  - Is Phytozome interested in hosting a pangenome resources?
+- NCBI SRA: raw data + experimental metadata
+  - NEON has worked with SRA on data/metadata sharing, keep in touch with them
+- Others?
+
+Other questions / ideas
+
+- How to get from genbank to related
+
+NEON: providing metagenomic data, processed and made available to the public w/ mgrast; marker gene sequences will be hosted in SRA / not available w/in NEON portal but available from external repository. Genomic standard meeting next week, working on environmental soil meta-data package for Mixs [http://gensc.org/mixs/submit-mixs-metadata/](http://gensc.org/mixs/submit-mixs-metadata/)
+
+NEON has started using EML to begin documenting sensor and observational data (currently online at [http://data.neonscience.org](http://data.neonscience.org) but not pretty). May begin doing this w/ soil samples.
+
+Action items:
+
+### **References**
+
+- Genomics pipeline documentaiton [https://github.com/terraref/documentation/blob/master/genomics\_pipeline.md](https://github.com/terraref/documentation/blob/master/genomics_pipeline.md)
+- Genomics data formats: [terraref/reference-data/19](https://github.com/terraref/reference-data/issues/19)
+- Pipeline implementation: [terraref/computing-pipeline/issues/37](https://github.com/terraref/computing-pipeline/issues/37)
+- Using CoGe [terraref/computing-pipeline/issues/41](https://github.com/terraref/computing-pipeline/issues/41)