Thoughts on sequencing strategy

Lex Nederbragt (corr) et al.

When setting up a strategy for sequencing/assembly these are valuable to know:

  • the goal of the project, e.g.
  • gene-mining
  • presence/absence of genes
  • long scaffolds for synteny
  • reference genome-standard (whatever that is)
  • strain variation/haplotying
  • genome size
  • genome complexity, i.e. repeat content and level of heterozygosity
  • number of chromosomes, extrachromosomal elements
  • can a pure sample be obtained or will there be contaminating DNA?
  • how much DNA can be obtained from a single individual/clonal line or will it be necessary to use DNA from a mix of different individuals (read: different genomes)?
  • is there sequencing data available from the same individual or species?
  • how close is the most closely related reference genome?

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Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.

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