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A Genome Sequence Analysis System Built With Hypertable

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The document describes a genome sequence analysis system built using Hypertable to store and analyze genomic sequence data from biological samples. The system uses a NoSQL database and schema design to store taxonomic data, sequence reads, genes and alignments. It enables applications like novel virus discovery, pathogen discovery in cancer samples, and a future depletion array technique.

Technology
1 of 27
A Genome Sequence Analysis System Built with Hypertable Doug Judd CEO, Hypertable, Inc.
Application Development Team ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What is Hypertable? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Hypertable Deployments
Why NoSQL?
Source: Nature 458, 719-724 (2009)
Source: wired.com, February 2011
Genomics 101
Base Pair (aka “base”) ,[object Object],[object Object],[object Object],[object Object],[object Object]
Gene ,[object Object],[object Object],[object Object],[object Object],[object Object]
Biological Samples ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Example Reads File GTGGATAGGGGGAGACTAATGTAGTATGATTATCATCATCAACAGAAGCTATGACACCAGGATAAA CATTTCTTATTGCTGAAAGTATTCTATTGTAGAGATGTACCACAATTTGGTTTCTGGTTTTGTATT GGGAGGATACTAGGGATTACTGAAGCCAACTTTGCAGACTCATACATTTGACTAGACACAGCC ACATTACAGTTTTCTGAGGAAAATTCTTAAGATGTTACCCCAAAACATAGCATTTTAAATTAAAAC GGACCGGCTGAAGCCATGGCAGAAGAACATAAATTGTGAAGATTTCATGGGCATTTATTAGTT GGAAGTGATAAGTGTCCATGAAATCTTCACAATTTATGTTCAGAGATTGCAGTAAAGACAGGTGTA AAGACACAGCAAAGCTAAGAGGACCCAACACACGGTAGGGTCGGGGACCTTGGAGAAACATGG TGGCTTCTTCCTACATGCTTGTGATAGATGACCAAAAAACATTTGTTGAGTTGATGAATAGTACAA AAAAGGGGCGGATAATAAATGAAAAGGGAATGTGCTGTTATTTCCTACTAAGATCAGAAAGAG ATATAAACAAAAGCTGTCATCACTTAGGGACTTCAGCCACATAAAACAATGTCAGGCTAGTCACTT AGAGCTTTGGGACTAGTTGAGTGGCAGCTTAACAAAGCAACGCAATATCCATAGGGATTGGGG ATATTTACATCTAGTGGATTCTACCAGTATGGTGGTCTTATGTGGACTGCACGTGGTTTTCTAGTA AGATAGCAGCTCTTCCCAAATTTATTTATAATTGTGGCATTATTTATAATATCAAAATATTAT GTTGCCAAAGGAGATTAACATTTGAGTCAGTGGGCGGGGTAAGGCCGACCTACCCTTAATCTGGTG GAGAAAGAAGCTGCTAATGGAGTTTAAAAGGTTACTGTCATTAATGAAAAATAAATTTACAGC CAGACATTTATGAACAGAAATGGGAAAAACACACTAGGAAAGCACTGCAAAGACTAATCTGTCTTT AAAGGAGATAGAGTGACTCCAGGCCCCTTAGAAATGACTATACCTGGCAGAGCATGCCAACTG ATGGGCTCGAGTCCTCACAAATATGAATTCCCCCTAAGTCTTGAGAGGTCATTTGTGCATTTGGAA GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGTCATACTGCCCA GCGGGGTTTTTTTTTGTTTCATATTAACTTTAAAGTAGTTTTTTTCCATTTTGTGAAGAAAGACAT AAAGAACCAAGGCTAATAGTTGTTTGAGTTGTACTTACCATGTTGTTAAATGTCACCTCACAC CGCTGCCAGCCTATCAGAGCCGGGAATTACACCGTGCTTGGAGTTCTGGCACAGATCCACAGCTAC AGTTCTTCATTGTAAGAAATGGATGCTAACATGTAACAAGAAAACATCTGAAGGTTAAACTCA AATAAATGGGTTAATAGTTTGTCTTTCGGTCTTCATACTTTCAATATAAGTGGTTTACTTAGCCGA
Sequence Alignment ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Taxonomy ,[object Object],[object Object],[object Object],[object Object],[object Object]
GenBank ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Schema Design
Taxa Table ,[object Object],[object Object],CREATE TABLE Taxa (ID, Type, Children, Name); /1 ID 1 /1 ID :fullName /root /1 Type no rank /1 Children 1,10239,12884,12908,28384,131567 /1 Name root /1/10239 ID 10239 /1/10239 ID :fullName /root/Viruses /1/10239 Type superkingdom /1/10239 Children 12333,12429,12877,29258,35237, … /1/10239 Name Viruses /1/10239/12333 ID 12333 /1/10239/12333 ID :fullName /root/Viruses/unclassified phages /1/10239/12333 Type no rank /1/10239/12333 Children 12340,12347,12366,12371,12374, … /1/10239/12333 Name unclassified phages
Reads Table ,[object Object],[object Object],CREATE TABLE Reads (Sequence, Quality, GeneKey, Comments); AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Sequence ATCGCACCATTGAACTCCAGTC... AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Quality eeaeeeede_Ycc]dcacab... AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Comments :qualityFilter 11071815... AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Sequence GGCTTACGCCTGTAATCCCAGC... AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Quality gfee_cgggegggecggggegc... AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 GeneKey :gnl|GNOMON|1320663.m 11... AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 Sequence AGGATACGGAAGGCCCAAGGAG... AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 Quality cdd`dffffffgffgggegf^e... AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 GeneKey :chr10 110718151643.1308... AbCam1_100_ACAGTG,HWI...80#ACAGTG/1 Sequence ACGGAAGAGCACACGTCTGAAC... AbCam1_100_ACAGTG,HWI...80#ACAGTG/1 Quality cbccb[^WUb]_b`_[bR_]... AbCam1_100_ACAGTG,HWI...80#ACAGTG/1 Comments :qualityFilter 11071815... AbCam1_100_ACAGTG,HWI...88#ACAGTG/1 Sequence GAACTCCAGTCACACAGTGATC... AbCam1_100_ACAGTG,HWI...88#ACAGTG/1 Quality eeeeeeeeeeeceeeeeaeeTQ... AbCam1_100_ACAGTG,HWI...88#ACAGTG/1 Comments :qualityFilter 11071815...
Genes Table ,[object Object],[object Object],CREATE TABLE Genes (Sequence, TaxID, ID, ReadID); 1000075 Sequence GAATTCCATGGCAGTAAAACATCTTCCCTTC… 1000075 TaxID 9606 1000075 ID :name HSLFBPS6 Human fructose-1,6-biphosphatase 1000075 ReadID :0310.Lane8big,HWI-EAS355:8:91:1231:1315#0/1 … 1000075 ReadID :0908.Mexus2.TATTAT,SCS:1:22:395:324#0/1_TA … 1000075 ReadID :0916.Enceph2,SCS:6:24:1519:513#0/1 1000075 ReadID :0916.Mexus,SCS:1:22:410:248#0/1 1000075 ReadID :0916.MonkeyAdeno,SCS:2:17:811:769#0/1 1000075 ReadID :0916.MonkeyAdeno,SCS:2:21:1132:1067#0/1 1000075 ReadID :0916.MonkeyAdeno,SCS:2:24:1207:492#0/1 1000075 ReadID :0916.MonkeyAdeno,SCS:2:33:1138:547#0/1 1000075 ReadID :0916.Parecho,SCS:3:4:679:1416#0/1|1 1000075 ReadID :HIV.HIV18_Lane7.s_7_sequence.AAA,SCS:7:30:688 … 1000075 ReadID :HIV.HIV18_Lane7.s_7_sequence.AAA,SCS:7:30:688 … 1000075 ReadID :HIV.HIV18_Lane7.s_7_sequence.unbiased,SCS:7:30 …
Monitoring Table Overview
Applications
Novel Virus Discovery ,[object Object],[object Object],[object Object],[object Object],[object Object]
Novel Virus Discovery Algorithm Detail ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Pathogen Discovery in Cancer Samples ,[object Object],[object Object]
Taxonomic Tree Viewer ,[object Object],[object Object],[object Object]
Depletion Array (future) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The End Questions?

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A Genome Sequence Analysis System Built With Hypertable

  • 1. A Genome Sequence Analysis System Built with Hypertable Doug Judd CEO, Hypertable, Inc.
  • 2.
  • 3.
  • 6. Source: Nature 458, 719-724 (2009)
  • 9.
  • 10.
  • 11.
  • 12. Example Reads File GTGGATAGGGGGAGACTAATGTAGTATGATTATCATCATCAACAGAAGCTATGACACCAGGATAAA CATTTCTTATTGCTGAAAGTATTCTATTGTAGAGATGTACCACAATTTGGTTTCTGGTTTTGTATT GGGAGGATACTAGGGATTACTGAAGCCAACTTTGCAGACTCATACATTTGACTAGACACAGCC ACATTACAGTTTTCTGAGGAAAATTCTTAAGATGTTACCCCAAAACATAGCATTTTAAATTAAAAC GGACCGGCTGAAGCCATGGCAGAAGAACATAAATTGTGAAGATTTCATGGGCATTTATTAGTT GGAAGTGATAAGTGTCCATGAAATCTTCACAATTTATGTTCAGAGATTGCAGTAAAGACAGGTGTA AAGACACAGCAAAGCTAAGAGGACCCAACACACGGTAGGGTCGGGGACCTTGGAGAAACATGG TGGCTTCTTCCTACATGCTTGTGATAGATGACCAAAAAACATTTGTTGAGTTGATGAATAGTACAA AAAAGGGGCGGATAATAAATGAAAAGGGAATGTGCTGTTATTTCCTACTAAGATCAGAAAGAG ATATAAACAAAAGCTGTCATCACTTAGGGACTTCAGCCACATAAAACAATGTCAGGCTAGTCACTT AGAGCTTTGGGACTAGTTGAGTGGCAGCTTAACAAAGCAACGCAATATCCATAGGGATTGGGG ATATTTACATCTAGTGGATTCTACCAGTATGGTGGTCTTATGTGGACTGCACGTGGTTTTCTAGTA AGATAGCAGCTCTTCCCAAATTTATTTATAATTGTGGCATTATTTATAATATCAAAATATTAT GTTGCCAAAGGAGATTAACATTTGAGTCAGTGGGCGGGGTAAGGCCGACCTACCCTTAATCTGGTG GAGAAAGAAGCTGCTAATGGAGTTTAAAAGGTTACTGTCATTAATGAAAAATAAATTTACAGC CAGACATTTATGAACAGAAATGGGAAAAACACACTAGGAAAGCACTGCAAAGACTAATCTGTCTTT AAAGGAGATAGAGTGACTCCAGGCCCCTTAGAAATGACTATACCTGGCAGAGCATGCCAACTG ATGGGCTCGAGTCCTCACAAATATGAATTCCCCCTAAGTCTTGAGAGGTCATTTGTGCATTTGGAA GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGTCATACTGCCCA GCGGGGTTTTTTTTTGTTTCATATTAACTTTAAAGTAGTTTTTTTCCATTTTGTGAAGAAAGACAT AAAGAACCAAGGCTAATAGTTGTTTGAGTTGTACTTACCATGTTGTTAAATGTCACCTCACAC CGCTGCCAGCCTATCAGAGCCGGGAATTACACCGTGCTTGGAGTTCTGGCACAGATCCACAGCTAC AGTTCTTCATTGTAAGAAATGGATGCTAACATGTAACAAGAAAACATCTGAAGGTTAAACTCA AATAAATGGGTTAATAGTTTGTCTTTCGGTCTTCATACTTTCAATATAAGTGGTTTACTTAGCCGA
  • 13.
  • 14.
  • 15.
  • 17.
  • 18.
  • 19.
  • 22.
  • 23.
  • 24.
  • 25.
  • 26.

Editor's Notes

  1. Improvements in the rate of DNA sequencing over the past 30 years and into the future