A survey of sequence alignment algorithms for next-generation sequencing

A survey of sequence alignment algorithms for next-generation sequencing.

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Here's a good review of current (short-read) sequence alignment algorithms applied to next-generation sequencing technology. It describes some of the fundamental design choices made during sequence alignment. Both hash-based and BWT-based algorithms are covered. There is also an interesting discussion of need for gapped alinment (shot over the bow of bowtie?). There are also brief discussions of color space read, long reads, bisulfite-treated reads, spliced reads, re-alignment, and a general overview of popular alignment software.

Anyhow, it is a good review so check it out.