New Sequencers Not Yet Able to Capture All Structural Variation, Scientists Say | GenomeWeb
Research initiatives such as the 1,000 Genomes Project have started to use new high-throughput sequencing technologies to map structural variations in individual human genomes and to detect SNPs and small indels.
But some scientists caution that the new sequencing platforms may miss a significant fraction of structural variants, and that older-generation technologies such as fosmid-based sequencing and microarrays will still be needed, at least for the time being.

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