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Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform Heng Li and Richard Durban

Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform Heng Li and Richard Durban. CSC2431 February 3 rd 2010 Alecia Fowler. Short Read Alignment. SPEED AND ACCURACY. Burrows Wheeler Aligner . OVERVIEW: based on backward search and Burrows-Wheeler Transform (BWT)

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Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform Heng Li and Richard Durban

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  1. Fast and Accurate Short Read Alignment with Burrows-Wheeler TransformHeng Li and Richard Durban CSC2431 February 3rd 2010 Alecia Fowler

  2. Short Read Alignment SPEED AND ACCURACY

  3. Burrows Wheeler Aligner OVERVIEW: based on backward search and Burrows-Wheeler Transform (BWT) FEATURES: performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality PLATFORM: Illumina; SOLiD; 454; Sanger PROS: fast CONS: short read algorithm is slow for long reads and reads with high error rate

  4. Prefix trie X = GOOGOL$ “G” “GO” “GOO” “GOOG” “GOOGO” “GOOGOL”

  5. Burrows-Wheeler Transform (BWT) • Algorithm used for data compression • Output is easier to compress as it groups similar symbols together

  6. Suffix array interval and sequence alignment

  7. Exact and Inexact Matching • Has to account for mismatches or gaps in the reads • the BWT index of the reverse reference sequence narrows the search space W = LOL X = GOOGOL$

  8. Evaluation: Simulated Data • Simulated reads from human genome • One million pairs of different lengths • Mapped to the human genome • BWA was found to be more accurate than Bowtie and SOAPv2 • Would need to sacrifice mapping quality in order to increase speed

  9. Evaluation: Real Data • 12.2 million pairs of 51bp reads from a male genome • Mapped to human genome and a human-chicken hybrid reference • Had high speed and accuracy for both

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