'Burrows wheeler' diaporamas de présentation

Short Read Mapping On Post Genomics Datasets

Short Read Mapping On Post Genomics Datasets. Adapted from Langmead Trapnell, Pop, Salzberg. Cedric Notredame. DATA. The Data: FASTQ. Data SAM. The Data: BAM. The Data: SAM/BAM. SAM/BAM Tools. SAM/BAM: Visualization. SAM/BAM: Visualization. SHORT READS. Short Read Applications.

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Short Read Mapping On Post Genomics Datasets

Short Read Mapping On Post Genomics Datasets. Adapted from Langmead Trapnell, Pop, Salzberg. Cedric Notredame. DATA. The Data: FASTQ. The Data: CSFASTQ (ABI). Data SAM. The Data: BAM. The Data: SAM/BAM. SAM/BAM Tools. SAM/BAM: Visualization. SAM/BAM: Visualization. SHORT READS.

970 views • 75 slides

Short Read Mapping On Post Genomics Datasets

Short Read Mapping On Post Genomics Datasets. Adapted from Langmead Trapnell, Pop, Salzberg. Cedric Notredame. DATA. The Data: FASTQ. The Data: CSFASTQ (ABI). Data SAM. The Data: BAM. The Data: SAM/BAM. SAM/BAM Tools. SAM/BAM: Visualization. SAM/BAM: Visualization. SHORT READS.

755 views • 75 slides

Introduction to Modeling and Algorithms in Life Sciences

Introduction to Modeling and Algorithms in Life Sciences. Ananth Grama Purdue University http://www.cs.purdue.edu/homes/ayg. Acknowledgements. To various sources, including Profs. Mehmet Koyuturk, Michael Raymer, Wiki sources (pictures), and other noted attributions.

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15-499:Algorithms and Applications

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IMPLEMENTATION OF A DIGITAL COMMUNUCATION SYSTEM

Data File. Source Coder. Encryption System. Channel FEC coder. AWGN Channel. Steganography System. IMPLEMENTATION OF A DIGITAL COMMUNUCATION SYSTEM. Murad S. Qasim & Mohammad Hamid. Dr. Allam Mousa. Introduction.

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Data Compression

Data Compression. Lempel-Ziv algorithms Burrows-Wheeler. Lempel-Ziv Algorithms. LZ77 (Sliding Window) Variants: LZSS (Lempel-Ziv-Storer-Szymanski) Applications: gzip, Squeeze, LHA, PKZIP LZ78 (Dictionary Based) Variants: LZW (Lempel-Ziv-Welch), LZC (Lempel-Ziv-Compress)

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CS 6293 Advanced Topics: Translational Bioinformatics

CS 6293 Advanced Topics: Translational Bioinformatics. Next-generation sequencing - Mapping short reads. Short read mapping. Input: A reference genome A collection of many 25-100bp tags (reads) User-specified parameters Output: One or more genomic coordinates for each tag

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CS 5263 & CS 4593 Bioinformatics

CS 5263 & CS 4593 Bioinformatics. Next-generation sequencing - Mapping short reads. Short read mapping. Input: A reference genome A collection of many 25-100bp tags (reads) User-specified parameters Output: One or more genomic coordinates for each tag

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CPS 296.3:Algorithms in the Real World

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CPS 296.3:Algorithms in the Real World

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CPS 296.3:Algorithms in the Real World

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High Throughput Sequencing

High Throughput Sequencing. Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520. First Generation. Sanger Sequencing: sequencing and detection 2 different steps: 384 * 1kb / 3 hours. Second Generation. Massively parallel sequencing by synthesis

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15-853:Algorithms in the Real World

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Mapping NGS sequences to a reference genome

Mapping NGS sequences to a reference genome. Why?. Resequencing studies (DNA) Structural variation SNP identification RNAseq Mapping transcripts to a genome sequence Genome annotation Transcript enumeration Identification of splice junctions/variants. Blast is too slow.

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Short read alignment

Short read alignment. BNFO 601. Short read alignment. Input: Reads: short DNA sequences usually up to 100 base pairs (bp) produced by a sequencing machine Reads are fragments of a longer DNA sequence present in the sample given as input to the machine Usually number in the millions

254 views • 11 slides