The purpose of this tutorial is to guide users from the raw FASTQ files produced by the sequencer to obtaining aligned short reads to human and non-human (pathogen) references in the sequence Alignment/Map (SAM) report format. In this tutorial we will consider Illumina single end reads although most of this tutorial applies to pair end reads as well.
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A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms
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