#+title: Community developed variant calling pipelines
#+author: Brad Chapman \\ Bioinformatics Core, Harvard School of Public Health \\ https://github.com/chapmanb
#+date: 22 October 2013

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* Challenges

** Complex, rapidly changing pipelines

[[./images/gatk_changes.png]]

** Large number of specialized dependencies

#+ATTR_LATEX: :width .5\textwidth
[[./images/huge_seq.png]]

[[https://github.com/StanfordBioinformatics/HugeSeq]]

** Quality differences between methods

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[[./images/gcat_comparison.png]]

[[http://www.bioplanet.com/gcat]]

** Scaling on full ecosystem of clusters

[[./images/schedulers.png]]

* Solution

** Solution

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[[./images/community.png]]
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\scriptsize
[[http://www.amazon.com/Community-Structure-Belonging-Peter-Block/dp/1605092770]]
\normalsize

** Overview

#+ATTR_LATEX: :width 1.0\textwidth
[[./images/bcbio_nextgen_highlevel.png]]

** Development goals

- Quantifiable
- Analyzable
- Reproducible
- Scalable
- Community developed
- Accessible

* Arvados complementary

** Quantify quality

[[./images/minprep-callerdiff.png]]

- Reference materials: [[http://www.genomeinabottle.org/]]
- Quantification details: [[http://j.mp/bcbioeval2]]

** Query and analyze

#+ATTR_LATEX: :width 1.0\textwidth
[[./images/gemini.png]]

\vspace{0.5cm}
GEMINI: [[https://github.com/arq5x/gemini]]

** Automated installation

- Single biggest software problem: running for the first time
- Bootstrap from bare machine to ready-to-go pipeline
- Builds off existing installation work: CloudBioLinux, Homebrew
- Real life benchmark example data

[[http://cloudbiolinux.org]]

[[https://bcbio-nextgen.readthedocs.org]]

* Arvados overlap

** Provenance

- Current approaches
   - Full logging -- command lines and debugging
   - Third party version tracking
   - Virtual machines
- Long term plans
   - Keep
   - Metadata + traceability

** Parallel scaling

[[./images/parallel-clustertypes.png]]

- Infrastructure details: [[http://j.mp/bcbioscale]]
- IPython: \scriptsize [[http://ipython.org/ipython-doc/dev/parallel/index.html]] \normalsize
- Crunch: compute + distributed filesystems

* Summary

** Accessible

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[[./images/dtc_genomics.jpg]]
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[[http://exploringpersonalgenomics.org/]]

** Summary

- Community developed pipelines > challenges
- Focus
  - Assessing quality: good science
  - Analysis: enable exploration
  - Scalability: finish in time
  - Reproducibility: show your work
- Widely accessible

[[https://github.com/chapmanb/bcbio-nextgen]]
