"BaseSpace Apps- Is One Enough?' Biomatters' CTO D.Matt Landry on Bioinformatics 3.0
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Biomatters' CTO D.Matt Landry gave a presentation titled 'BaseSpace Apps- Is One Enough?' at Illumina's BaseSpace Worldwide Developer meeting. #basedev2013, #bioinformatics 3.0
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"BaseSpace Apps- Is One Enough?' Biomatters' CTO D.Matt Landry on Bioinformatics 3.0
- 1. BaseSpace Apps IS ONE ENOUGH? D Matthew Landry, CTO dmlandry@biomatters.com dmlandry ! ILMN BaseSpace Worldwide Developer’s Mtg, 21 Oct 2013 This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License
- 2. Disclosure I have no actual or potential conflict of interest in relation to this presentation. Except the obvious:
- 3. Bioinformatics 1.0 ⟶ 3.0 Technology like BaseSpace We almost got it wrong
- 5. #!/usr/bin/env bash /bin/BWA/bwa aln -f /output/FOO.sai -t 3 /seq/ REFERENCE/human_18.fasta /seq/FQ/FOO.sanger.fq /bin/BWA/bwa samse -f /output/FOO.sam /seq/REFERENCE/ human_18.fasta /output/FOO.sai /seq/FQ/FOO.sanger.fq /bin/SAMTOOLS/samtools import /seq/REFERENCE/ human_18.fasta /output/FOO.sam /output/FOO.bam /bin/SAMTOOLS/samtools sort /output/FOO.bam /output/ FOO.sorted /bin/SAMTOOLS/samtools index /output/FOO.sorted.bam / output/FOO.sorted.bam.bai java -jar /bin/GTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /seq/REFERENCE/ human_18.fasta -I /output/FOO.sorted.bam -o /output/ FOO.intervals java -jar /bin/GTK/GenomeAnalysisTK.jar -T IndelRealigner -R /seq/REFERENCE/human_18.fasta -I / output/FOO.sorted.bam -targetIntervals /output/ FOO.intervals --output /output/ FOO.sorted.realigned.bam /bin/SAMTOOLS/samtools index /output/ FOO.sorted.realigned.bam /output/ FOO.sorted.realigned.bam.bai
- 7. Features - Genome browser - Annotation tracks - Genome assembly - Contig reporting - Read mapping - SNV detection - CNV detection - Differential expression - Microarray, RNA-seq - Epigenomics, ChIP-seq - NGS demultiplexing - DNA/RNA prediction - Primer design - In silico PCR - Molecular cloning - NCBI searching ...
- 11. How does this change the way we build apps?
- 14. No desktop limits Data quanta increasing Structured pipelines
- 16. Foundation platform Apply best-in-class tools Channel to users
- 22. Targeted Computational Dx for applied laboratory genomics
- 24. Is one App enough?
- 25. One is not enough.