SNAP is from 2-5x faster than commonly used aligners like BWA-mem2 and Bowtie2, and 20x-nearly 30x faster than Novoalign. This is a computationally challenging problem because reference genomes are big (the human genome is over 3 billion base pairs long) and are often highly repetitive. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and determines where, how well and how unambiguously they match to a given reference genome. SNAP is a program that is part of a gene sequencing pipeline.
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