Library preparation and data analysis packages for rapid genome sequencing.
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.
Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing (CGRB), Oregon State University, Corvallis, OR, USA.
Kyle R
KR
Pomraning
Kristina M
KM
Smith
Erin L
EL
Bredeweg
Lanelle R
LR
Connolly
Pallavi A
PA
Phatale
Michael
M
Freitag
D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics; D004260:DNA Repair; D020869:Gene Expression Profiling; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013010:Sonication; D013223:Statistics as Topic / Q000379:methods*; D013997:Time Factors
D004247:DNA