Parallel Implementation of BWT Under the Guidance of : Prof. Kolin Paul Presented By: Lalchand Gaurav Jain.

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Presentation transcript:

Parallel Implementation of BWT Under the Guidance of : Prof. Kolin Paul Presented By: Lalchand Gaurav Jain

Application Domain & objective Use of Bwt in Sequence assembly Bwt Implementation on GPU Bwt Implementation for larger Genome Comparative study Agenda

Application Domain & objective Use of Bwt in Sequence assembly Bwt Implementation on GPU Bwt Implementation for larger Genome Comparative study Agenda

Application Domain & objective Use of Bwt in Sequence assembly Bwt Implementation on GPU Bwt Implementation for larger Genome Comparative study Agenda

Application Domain & objective Use of Bwt in Sequence assembly Bwt Implementation on GPU Bwt Implementation for larger Genome Comparative study Agenda

Application Domain & objective Use of Bwt in Sequence assembly Bwt Implementation on GPU Bwt Implementation for larger Genome Comparative study Agenda

Application Domain & Objective To present an efﬁcient implementation of BWT for larger Genome. Analyzing Gene expression Mapping variations between individuals Mapping homologous Proteins Assembling Genome of Organism

Indexing Contigs Use of Bwt in Sequence assembly SGA Intermediate size :10^18 Genome e

9 Burrows-Wheeler Transform 5$ACGTA 4A$ACGT 3TA$ACG 2GTA$AC 1CGTA$A 0ACGTA$ Input: A C G T A $ Output: A T $ A C G indices: $ACGTA 4A$ACGT 0ACGTA$ 1CGTA$A 2GTA$AC 3TA$ACG indices: Bwt[i] = ref [ SA[i] -1] {Bwt[i] = $ when S(i)= 0}

 Implemented Bwt on GPU  Bitonic sort  Implemented Bwt for larger genome  In mutipass (GPU and CPU) Work Done

Why Bitonic ??... Concatenations of two sub-sequences sorted in opposite directions A cyclic shift of elements Implemented by comparator networks Work in place No Communication Naturally suitable for SIMD architectures Each thread executing same code but different data O(log 2 n) time and O(nlog 2 n) work

Bwt Procedure For larger Genome Genome Read & store (CPU) Bitonic_sort_step Calcualte Gap array Merge Suffix array (CPU) Calcualte Gt array Suffix - > BWT Suffix array (CPU) 2*CHUNK

Comparison between Parallel BWT(GPU) and serial BWT (CPU) Serial Bwt : Does not work for large files

Comparison between Parallel BWT (GPU) and Parallel BWT (CPU)

Evaluation for larger Genome

References : Lightweight Data Indexing and Compression in External Memor Paolo Ferragina 1, Travis Gagie2, and Giovanni Manzini Fast in-place sorting with CUDA based on bitonic sort :Hagen Peters Rapid Parallel Genome Indexing with MapReduce :Rohith K. Menon M. Burrows and D. Wheeler. A Block-Sorting Lossless Data Compression Algorithm. Technical report Lightweight Data Indexing and Compression in External Memory :Paolo Ferragina Parallel Lossless Data Compression on the GPU : Yao Zhang

Thanks