Library preparation and data analysis packages for rapid genome sequencing

Methods Mol Biol. 2012;944:1-22. doi: 10.1007/978-1-62703-122-6_1.


High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation
  • DNA / genetics
  • DNA Repair
  • Gene Expression Profiling
  • Gene Library*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • INDEL Mutation / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA / methods*
  • Software
  • Sonication
  • Statistics as Topic / methods*
  • Time Factors


  • DNA