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  • Special Topics



  • Exercises

    Beyond the Genome Challenges
    BTG11: Viral Insertion  Identify the virus in a cancer exome sequencing project
    BTG12: Digital Encoding  Identify the secret message inserted into a microbial genome
    BTG13: Metagenomics Variants  Identify the secret message encoded as variants within a metagenomics sample
     
    Genomics
    Read Mapping  Read mapping, identifying variants, running BWA/SAMTools
    RNA-seq Analysis  Read mapping, computing expression, running Bowtie/Tophat/Cufflinks
    Genome assembly  De novo assembly and error correction, whole genome alignment
    Coverage analysis  Coverage analysis using plane-sweep algorithms
     
    Probability and Statistics
    Rolling a die  Uniform Random Probability
    Flipping a coin  Binimal and Normal Distributions
    Marbles in jars  Poisson Distribution
    Throwing darts  Exponential Distribution
     
    Computing
    Python Basics 1  Introduction to python, variables, lists, conditions, loops
    Python Basics 2  Brute force search, dictionaries, motif finding
    Hadoop  Getting started with Hadoop, kmer counting and word analysis
     



    Essential Resoures

    Online Resources
    NCBI   PubMed, Genomes, Genbank, SRA
    UCSC Genome Browser   Interactive genome plots, coverage, annotations
    Galaxy   Interactive genome analysis (CSHL version)
    SeqAnswers   Forums and tutorials for genomics analysis
    Khan Academy   Videos and Tutorials on many science and mathematics related topics
    CiteULike   Social networking for citations and papers
    Rosalind   Programming and Bioinformatics exercises
    JHU Comp Genomics   iPython Notebooks of basic string algorithms
     
    FASTQ trimming and error correction
    FASTX-Tools   Filter and trim fastq files
    Quake   Error Correction of Short Reads
     
    Aligners and variant callers
    Bowtie/Bowtie2   Ultra-fast short read mapping with the BWT
    BWA   Feature rich short read alignment
    SAMTools   SAM/BAM alignment filtering and scoring
    Picard   SAM/BAM alignment filtering
    BedTools   Slice and dice genomics intervals
    GATK   Variant calling
    Hydra   Structural Variations calling with discordant pair analysis
     
    RNA-seq Analysis
    TopHat   Spliced alignment for RNA-seq
    Cufflinks   Transcript assembly and quantification
    Trinity   De novo transcript assembly and quantification
     
    Assembly and Whole Genome Alignment
    ALLPATHS-LG   Assembly of short reads
    SOAPdenovo   Assembly of short reads
    Celera Assembler   Assembly of long reads
    MUMmer   Whole Genome Alignment
    AMOS   Assembly and assembly related tools
     
    Statistics and Visualization
    Canopy   Python Integrated Development Environment
    matplotlib   Visualization in python
    R   Statistics and visualization
    Circos   Circular plots of genomes and other data
    Graphviz   Layout and render graphs
    Weka   Data Mining and classification
    IGV   Interactive Genomics Viewer for short reads