| 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 |
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| 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 |
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| 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 |
| Negative Binomial | | Negative Binomial Distribution |
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| 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 |
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| 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 |
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| FASTQ trimming and error correction |
| FASTX-Tools | | Filter and trim fastq files |
| Quake | | Error Correction of Short Reads |
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| 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 |
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| RNA-seq Analysis |
| TopHat | | Spliced alignment for RNA-seq |
| Cufflinks | | Transcript assembly and quantification |
| Trinity | | De novo transcript assembly and quantification |
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| 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 |
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| 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 |
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