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Presentation for Mt Sinai workshop

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1 parent fd187e1 commit c90dc93985774cb06565a3b4719a976033980bc0 @chapmanb committed Dec 9, 2013
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+#+title: Community based approaches to scaling variant calling pipelines
+#+author: Brad Chapman \\ Bioinformatics Core, Harvard School of Public Health \\ https://github.com/chapmanb \\ http://j.mp/bcbiolinks
+#+date: 10 December 2013
+
+#+OPTIONS: toc:nil H:2
+
+#+startup: beamer
+#+LaTeX_CLASS: beamer
+#+latex_header: \usepackage{url}
+#+latex_header: \usepackage{hyperref}
+#+latex_header: \hypersetup{colorlinks=true}
+#+BEAMER_THEME: default
+#+BEAMER_COLOR_THEME: seahorse
+#+BEAMER_INNER_THEME: rectangles
+
+* 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
+
+#+ATTR_LATEX: :width .7\textwidth
+[[./images/gcat_comparison.png]]
+
+[[http://www.bioplanet.com/gcat]]
+
+** Scaling on full ecosystem of clusters
+
+[[./images/schedulers.png]]
+
+* Solution
+
+** Solution
+
+#+BEGIN_CENTER
+#+ATTR_LATEX: :width .5\textwidth
+[[./images/community.png]]
+#+END_CENTER
+
+\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
+
+\Large
+
+- Community developed
+\vspace{0.075cm}
+- Quantifiable
+\vspace{0.075cm}
+- Scalable
+
+\normalsize
+
+* bcbio-nextgen highlights
+
+** Community: installation
+
+*** Automated Install :block:
+ :PROPERTIES:
+ :BEAMER_env: exampleblock
+ :END:
+ Bare machine to ready-to-run pipeline, tools and data
+
+- CloudBioLinux: [[http://cloudbiolinux.org]]
+- Homebrew: https://github.com/Homebrew/homebrew-science
+- Conda: http://j.mp/py-conda
+
+** Community: documentation
+
+[[./images/community-docs.png]]
+
+[[https://bcbio-nextgen.readthedocs.org]]
+
+** Community: contribution
+
+[[./images/community-contribute.png]]
+
+[[https://github.com/chapmanb/bcbio-nextgen]]
+
+** Quantify quality
+
+[[./images/minprep-callerdiff.png]]
+
+- Reference materials: [[http://www.genomeinabottle.org/]]
+- Quantification details: [[http://j.mp/bcbioeval2]]
+
+** Validation
+
+\Large
+- Unit tests for implementation and methods
+- Expand to:
+ - \large Cancer tumor/normal http://j.mp/cancer-var-chal
+ - Family/population calling
+ - Structural variations
+\normalsize
+
+* Scaling
+** Scaling overview
+
+[[./images/bcbio_parallel_overview.png]]
+
+- Infrastructure details: [[http://j.mp/bcbioscale]]
+- IPython: \scriptsize [[http://ipython.org/ipython-doc/dev/parallel/index.html]] \normalsize
+
+** Current target environment
+
+- Cluster scheduler
+ - SLURM
+ - Torque
+ - SGE
+ - LSF
+- Shared filesystem
+ - NFS
+ - Lustre
+- Local temporary disk
+ - SSD
+
+** Alignment parallelization
+
+[[./images/bcbio_align_parallel.png]]
+
+** Variant calling and BAM preparation parallelization
+
+[[./images/parallel-genome.png]]
+
+** Multicore parallelization
+
+*** BAM manipulation :block:
+ :PROPERTIES:
+ :BEAMER_env: exampleblock
+ :END:
+
+Sambamba \\
+https://github.com/lomereiter/sambamba
+
+
+\vspace{0.75cm}
+
+*** Prep analysis database (SQLite) :block:
+ :PROPERTIES:
+ :BEAMER_env: exampleblock
+ :END:
+
+GEMINI \\
+https://github.com/arq5x/gemini
+
+** Memory usage
+
+*** :B_columns:
+ :PROPERTIES:
+ :BEAMER_env: columns
+ :END:
+
+**** Configuration :block:
+ :PROPERTIES:
+ :BEAMER_opt: t
+ :BEAMER_col: 0.5
+ :END:
+
+/Configuration/
+
+#+begin_src
+bwa:
+ cmd: bwa
+ cores: 16
+samtools:
+ cores: 16
+ memory: 2G
+gatk:
+ jvm_opts: ["-Xms750m", "-Xmx2750m"]
+#+end_src
+
+**** Batch file :block:
+ :PROPERTIES:
+ :BEAMER_opt: t
+ :BEAMER_col: 0.5
+ :END:
+
+/Batch file/
+
+#+begin_src
+#PBS -l nodes=1:ppn=16
+#PBS -l mem=45260mb
+#+end_src
+
+** Filesystem IO
+
+*** Pipes and streaming algorithms :block:
+ :PROPERTIES:
+ :BEAMER_env: exampleblock
+ :END:
+
+#+begin_src python :exports code
+("{bwa} mem -M -t {num_cores} -R '{rg_info}' -v 1 "
+ "{ref_file} {fastq_file} {pair_file} "
+ "| {samtools} view -b -S -u - "
+ "| {samtools} sort -@ {num_cores} -m {max_mem} "
+ "- {tx_out_prefix}")
+#+end_src
+
+** Dell System
+
+[[./images/dell-ai-hpc.png]]
+
+*** Glen Otero, Will Cottay :block:
+ :PROPERTIES:
+ :BEAMER_env: block
+ :END:
+ http://dell.com/ai-hpc-lifesciences
+
+** Evaluation details
+
+*** :B_columns:
+ :PROPERTIES:
+ :BEAMER_env: columns
+ :END:
+
+**** Samples :BMCOL:
+ :PROPERTIES:
+ :BEAMER_col: 0.5
+ :END:
+
+Samples
+
+- 60 samples
+- 30x whole genome
+- Illumina
+- Family-based calling
+
+**** System :BMCOL:
+ :PROPERTIES:
+ :BEAMER_col: 0.5
+ :END:
+
+System
+
+- 400 cores
+- 3Gb RAM/core
+- Lustre filesystem
+- Infiniband network
+
+** Timing: Alignment
+
+\begin{tabular}{lll}
+\hline
+Step & Time & Processes \\
+\hline
+Alignment preparation & 13 hours & BAM to fastq; bgzip; \\
+& & grabix index \\
+Alignment & 30 hours & bwa-mem alignment \\
+BAM merge & 7 hours & merge alignment parts \\
+Alignment post-processing & 9 hours & Calculate callable regions \\
+\hline
+\end{tabular}
+
+** Timing: Variant calling
+
+\begin{tabular}{lll}
+\hline
+Step & Time & Processes \\
+\hline
+Post-alignment & 12 hours & De-duplication \\
+BAM preparation & & \\
+Variant calling & 23 hours & FreeBayes \\
+Variant post-processing & 2 hours & Combine variant files; \\
+& & annotate: GATK and snpEff \\
+\hline
+\end{tabular}
+
+** Timing: Analysis and QC
+
+\begin{tabular}{lll}
+\hline
+Step & Time & Processes \\
+\hline
+BAM merging & 6 hours & Combine post-processed BAM file sections \\
+GEMINI & 3 hours & Create GEMINI SQLite database \\
+Quality Control & 5 hours & FastQC, alignment and variant statistics \\
+\hline
+\end{tabular}
+
+** Timing: Overall
+
+\Large
+- 4 1/2 total days for 60 samples
+- ~2 hours per sample at 400 cores
+- In progress: optimize for single samples
+\normalsize
+
+* Summary
+
+** Virtualization and reproducibility
+
+*** :B_columns:
+ :PROPERTIES:
+ :BEAMER_env: columns
+ :END:
+
+**** Amazon :BMCOL:
+ :PROPERTIES:
+ :BEAMER_col: 0.5
+ :END:
+
+[[./images/aws.png]]
+
+**** Docker :BMCOL:
+ :PROPERTIES:
+ :BEAMER_col: 0.5
+ :END:
+
+[[./images/homepage-docker-logo.png]]
+
+** Accessible
+
+#+BEGIN_CENTER
+#+ATTR_LATEX: :width .4\textwidth
+[[./images/dtc_genomics.jpg]]
+#+END_CENTER
+
+[[http://exploringpersonalgenomics.org/]]
+
+** Summary
+
+- Community developed pipelines > challenges
+- Focus
+ - Assessing quality: good science
+ - Community: easy to install and contribute
+ - Scalability: finish in time
+- Widely accessible
+
+[[https://github.com/chapmanb/bcbio-nextgen]]
+http://j.mp/bcbiolinks
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