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How to High Throughput Sequencing

Twenty years after the Human Genome Project, genomic sequencing is more accessible than ever before. Align and visualize next generation sequencing data with the High-Throughput Sequencing Alignment workflow, available in the Bioinformatics Toolbox™. An example data import, preprocessing, alignment and visualization workflow of Drosophila melanogaster (fruit fly) sequencing data is provided. Import FASTA and FASTQ files from your computer or directly from the NCBI GenBank database with just an ascension number and internet connection. Visualize read quality as a function of base pair as well as mean quality, GC content, and read length histograms to inform preprocessing decisions. Preprocess reads by filtering or trimming at the 5’ or 3’ end, by mean sequence quality, or a minimum percentage quality threshold. Align sequences to a reference using the Bioinformatics Toolbox Add-Ons bowtie, bowtie2 (demonstrated) or BWA. Store the alignment as a BioMapObject for visualization and convert from .sam to .bam format. Visualize the results on the Genomics Viewer Application, where additional alignments (.bam, .cram), feature annotations (.bed, .gff, .gff3, .gtf, structural variants (.vcf), copy number (.seg) and quantitative genomic data (.wig, .bigwig, .bedgraph) can be viewed simultaneously. Learn about the High Throughput Sequencing Alignment Workflow: Learn about the sequence alignment functions bowtie, bowtie2 and BWA supported on MATLAB: Learn more about visualization in the Genomics Viewer App: Introduction Import FASTA Data Preprocess Sequence Data Align Sequence Visualize Aligned Sequence

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