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Martine Zilversmit
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• Xin-zhuan Su • Sittiporn Pattaradilokrat • Sethu Nair • Yanwei Qi • Gordon Bullen NIH/ NIAID – Malaria Functional Genomics Section • Sebastian Gurevich McGill University Funding: National Institutes of Health Canadian Institutes of Health Research • Philip Awadalla University of Montreal https://github.com/parasite-genomics/Pipelines - 2.0 Coming in July 2014 zmartine@gmail.com ComPar: Genome Assembly, Variant Mapping, and Validation Pipelines Martine Zilversmit
ComPar: Genome Assembly, Variant Mapping, and Validation Pipelines https://github.com/parasite-genomics/Pipelines • BASH-scripted pipelines • Accurate variant prediction – SNPs – Small indels – Large indels (>17bp) – Focused regions of extreme divergence (35-70% amino acid identity) • In silico variant validation
Parameters: - Quality Metric and Cutoff - Number of variants per cluster - Maximum distance between variants within a cluster - Maximum distance between smaller clusters to merge into an HDR Finding Highly Divergent Regions – HDR Program VCF File False Positive Variants True Positive Variants HDR File: - Size of HDR - Position of HDR - Variants Contained Python - Stand-alone interactive or pipelined
NumberofVariants Position on “Chromosome” Dye-Terminator Sequenced Variation – 50 basepair Sliding window Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12
Predicted Variants – No filtering Based on Quality Metrics NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results
NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Quality 30 Cutoff Predicted Variants - Filtering Based on Quality Score ≥ 30 Cutoff
NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes Filtering Based on Consensus Quality (FQ) ≤ -100 Cutoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants FQ −100 Cuttoff
NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes Highly-Divergent Regions (HDRs) 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff
NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff Quality ≥ 30 Variants without Consensus Quality ≥ -100 Highly-Divergent Regions (HDRs) 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Quality 30, No HDRs
Characteristics of Highly Divergent Regions 33X 44.4% By265 55.6% N67 66.7% histone acetyltransferase GCN5, putative (GCN5) RNA-binding protein NOB1, putative Percent Identity DNA repair protein, putative 33X 41.4% By265 79.3% N67 51.7%
Characteristics of Highly Divergent Regions

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I evobio zilversmit_25jun14

  • 1. • Xin-zhuan Su • Sittiporn Pattaradilokrat • Sethu Nair • Yanwei Qi • Gordon Bullen NIH/ NIAID – Malaria Functional Genomics Section • Sebastian Gurevich McGill University Funding: National Institutes of Health Canadian Institutes of Health Research • Philip Awadalla University of Montreal https://github.com/parasite-genomics/Pipelines - 2.0 Coming in July 2014 zmartine@gmail.com ComPar: Genome Assembly, Variant Mapping, and Validation Pipelines Martine Zilversmit
  • 2. ComPar: Genome Assembly, Variant Mapping, and Validation Pipelines https://github.com/parasite-genomics/Pipelines • BASH-scripted pipelines • Accurate variant prediction – SNPs – Small indels – Large indels (>17bp) – Focused regions of extreme divergence (35-70% amino acid identity) • In silico variant validation
  • 3. Parameters: - Quality Metric and Cutoff - Number of variants per cluster - Maximum distance between variants within a cluster - Maximum distance between smaller clusters to merge into an HDR Finding Highly Divergent Regions – HDR Program VCF File False Positive Variants True Positive Variants HDR File: - Size of HDR - Position of HDR - Variants Contained Python - Stand-alone interactive or pipelined
  • 4. NumberofVariants Position on “Chromosome” Dye-Terminator Sequenced Variation – 50 basepair Sliding window Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12
  • 5. Predicted Variants – No filtering Based on Quality Metrics NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results
  • 6. NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Quality 30 Cutoff Predicted Variants - Filtering Based on Quality Score ≥ 30 Cutoff
  • 7. NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes Filtering Based on Consensus Quality (FQ) ≤ -100 Cutoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants FQ −100 Cuttoff
  • 8. NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes Highly-Divergent Regions (HDRs) 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff
  • 9. NumberofVariants Position on “Chromosome” NumberofVariants Position on “Chromosome” Comparing 2 Plasmodium Genomes 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Unfiltered Results Quality 30 Cutoff FQ −100 Cuttoff Quality ≥ 30 Variants without Consensus Quality ≥ -100 Highly-Divergent Regions (HDRs) 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600 4800 5000 5200 5400 5600 5800 6000 6200 6400 6600 6800 7000 7200 7400 7600 7800 8000 8200 8400 8600 8800 9000 9200 9400 9600 0 2 4 6 8 10 12 True Variants Quality 30, No HDRs
  • 10. Characteristics of Highly Divergent Regions 33X 44.4% By265 55.6% N67 66.7% histone acetyltransferase GCN5, putative (GCN5) RNA-binding protein NOB1, putative Percent Identity DNA repair protein, putative 33X 41.4% By265 79.3% N67 51.7%
  • 11. Characteristics of Highly Divergent Regions

Editor's Notes

  1. MAPPING, DEFINE! DE NOVO, DEFINE! SAY WHAT VARIANTS ARE
  2. Define highly divergent regions
  3. Define highly divergent regions
  4. Define highly divergent regions
  5. Define highly divergent regions
  6. Define highly divergent regions
  7. Define highly divergent regions