Algorithms for Next-gen Sequence Analysis

The field of next-gen sequence analysis is advancing so rapidly that new algorithms come out almost every day. Here we provide a broad categorization for such algorithms and describe critical challenges for each category. This will help us understand the approaches presented in various algorithms, when we look into each one in more detail.

Usually a scientist submits DNA samples for an organism to a core facility for sequencing and receives a large disk full of sequence data. The first categorization comes from whether the organism has a reference sequence. Second categorization comes from whether the sample is genomic or transcriptomic.

As a 2×2 matrix, the categories are

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