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How to map billions of short reads onto genomes

Nature Biotechnology volume 27, pages 455–457 (2009)Cite this article

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?

A new generation of DNA sequencers that can rapidly and inexpensively sequence billions of bases is transforming genomic science. These new machines are quickly becoming the technology of choice for whole-genome sequencing and for a variety of sequencing-based assays, including gene expression, DNA-protein interaction, human resequencing and RNA splicing studies1,2,3. For example, the RNA-Seq protocol, in which processed mRNA is converted to cDNA and sequenced, is enabling the identification of previously unknown genes and alternative splice variants; the ChIP-Seq approach, which sequences immunoprecipitated DNA fragments bound to proteins, is revealing networks of interactions between transcription factors and DNA regulatory elements4; and the whole-genome sequencing of tumor cells is uncovering previously unidentified cancer-initiating mutations5.

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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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Authors and Affiliations

  1. Cole Trapnell and Steven L. Salzberg are at the Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.,

    Cole Trapnell & Steven L Salzberg

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  1. Cole Trapnell
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  2. Steven L Salzberg
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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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