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Final Results Genome Assembly Team

Final Results Genome Assembly Team. Kelley Bullard, Henry Dewhurst, Kizee Etienne, Esha Jain, VivekSagar KR, Benjamin Metcalf, Raghav Sharma, Charles Wigington , Juliette Zerick. Original Pipeline. 454. Illumina DeNovo Allpaths LG SOAP DeNovo Velvet Taipan SUTTA.

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Final Results Genome Assembly Team

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  1. Final ResultsGenome Assembly Team Kelley Bullard, Henry Dewhurst, Kizee Etienne, Esha Jain, VivekSagar KR, Benjamin Metcalf, Raghav Sharma, Charles Wigington, Juliette Zerick

  2. Original Pipeline 454 • Illumina DeNovo • Allpaths LG • SOAP DeNovo • Velvet • Taipan • SUTTA • Hybrid DeNovo • Ray • MIRA Parameter optimization 454 raw reads Illumina raw reads Illumina hybrid • 454 DeNovo • Newbler • CABOG • SUTTA Process Illumina GAGE Statistical analysis Pre-processing 454 Evaluation Info. Illumina/ 454/ Hybrid DeNovo assembly Assemblers • GAGE • Hawk-eye Fastqc Prinseq NGS QC Assemblers Chosen Ref. Unmapped reads All possible combinations of the best 3 454 reads Illumina reads Read stats LEGEND contigs * 3 • Mimimus • MAIA Finished genome Scaffolds PRE-PROCESSING Align illumina reads against 454 contigs CONTIG MERGING Unmapped reads • MUMmer • PAGIT • Mauve Published Genomes from public databases Mac vector CLC wb V. vulnificus YJ016 V. vulnificus CMCP6 V. vulnificus MO6-24/O contigs Gap filling Nulceotide identity DENOVO ASSEMBLY GENOME FINISHING bwa Unmapped reads • GRASS • Built-in Align Illumina against the reference samstats contigs Compare mapping statistics Reference genome Illumina/(454?) reference based assembly Draft/ Finished genome • MUMmer • DNA Diff AMOScmp Reference evaluation Reference evaluation REFERENCE SELECTION REFERENCE BASED ASSEMBLY

  3. Read Visualization – spot the differences Comparison of 454 Reads for 08-2462 (low coverage) and 2541-90 (improved coverage) Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  4. Read Visualization - more is better! Nav 08-2462 454 reads compared to Nav 08-2462 Illumina reads. Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  5. Read Visualization – cousins or siblings? Nav_2541-90 and Vul_06-2432 (454 and Illumina reads) coverage comparison. Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  6. Data Quality Effect of pre-processing data (using prinseq)

  7. V. navarensis (454; non-preprocessed|pre-processed) Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  8. V. Vulnificus (454; non-preprocessed|preprocessed) • Metric Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  9. V. navarensis (Illumina; non-preprocessed|preprocessed) Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  10. V. vulnificus (Illumina; non-preprocessed|preprocessed) Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  11. Assembly Reference-guided and de-Novo

  12. Reference guided assembly Comparison of reference guided assembly vs de-novo assembly

  13. ARE – Assembly Score Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  14. Reference-guided vs de-Novo assembly ARE Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  15. Summary of Reference-guided assembly • Using V. vulnificus (CMCP6) reference strain • 84% coverage • De-Novo assemblers overall provided higher assembly score than reference based assembly Pipeline/Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  16. De Novo Assembly Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  17. De Novo Assembly Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  18. De Novo Assembly Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  19. De Novo Assembly Pipeline / Read Processing / Assembler Results / ContigMerging / Assembler Review / Pipeline / Final Results

  20. De-Novo Assembler Comparison (Optimal Parameters) ARE Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  21. Final Results – V. vulnificus CABOG Span Ratio Graph comparing assemblers on 3 criteria: Assembly Score, Span Ratio, 1/(Break Points). Higher score for all criteria are preferable. Newbler (dn) has been removed to show variance in other tools. Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  22. Final Results – V. vulnificus 1000/(Break Points) Graph comparing assemblers on 3 criteria: Assembly Score, Span Ratio, 1/(Break Points). Higher score for all criteria are preferable. Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  23. Summary of de-Novo results • OLC assemblers showed considerable differences in ARE than de-Brujin based assemblers • Cabog/Newblervs Soap de-Novo/Velvet • Hybrid assembler, Ray, did not perform as well in terms of assembly score Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  24. Merging-Vul_06-2432 Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  25. Merging-Nav_2541-90 Pipeline / Read Processing / Assembler Results / ContigMerging / Assembler Review / Pipeline / Final Results

  26. Assembler Review Mira worked as good as our merged contigs but it is impractical – 40hr run time BB = branch-and-bound; OLC = overlap consensus; DBG = de Bruijn Graph; ZEBRA Pipeline / Read Processing / Assembler Results / ContigMerging / Assembler Review/ Pipeline / Final Results

  27. Final Pipeline • Illumina DeNovo • Velvet 454 • Hybrid DeNovo • Ray • Mira 454 raw reads Illumina raw reads Illumina • 454 DeNovo • Newbler • CABOG hybrid Process Illumina Statistical analysis Pre-processing 454 Info. Illumina/ 454/ Hybrid DeNovo assembly Assemblers Fastqc Prinseq Assemblers Merge Ray –hyb/ Newbler Merge CABOG/Velvet MIRA-hyb LEGEND 454 reads Illumina reads Read stats contigs Mimimus Draft genome PRE-PROCESSING Align illumina reads against 454 contigs CONTIG MERGING contigs DENOVO ASSEMBLY Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  28. Splinter Pipeline 1 Pipeline 2 Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  29. Visualization Newbler Ray Hybrid Merged Pipeline / Read Processing / Assembler Results / Contig Merging / Assembler Review / Pipeline / Final Results

  30. Demo

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