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How to map billions of short reads onto genomes

Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?

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Figure 1: Two recent algorithmic approaches for aligning short (20–200-bp) sequencing reads.
Figure 2: RNA-Seq assays produce short reads sequenced from processed mRNAs.

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Correspondence to Cole Trapnell or Steven L Salzberg.

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Trapnell, C., Salzberg, S. How to map billions of short reads onto genomes. Nat Biotechnol 27, 455–457 (2009). https://doi.org/10.1038/nbt0509-455

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