title: A vertebrate case study of the quality of assemblies derived from next-generation sequences.
abstract: The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.
authors: The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA.
authors: Liang
authors: L
authors: Ye
authors: LaDeana W
authors: LW
authors: Hillier
authors: Patrick
authors: P
authors: Minx
authors: Nay
authors: N
authors: Thane
authors: Devin P
authors: DP
authors: Locke
authors: John C
authors: JC
authors: Martin
authors: Lei
authors: L
authors: Chen
authors: Makedonka
authors: M
authors: Mitreva
authors: Jason R
authors: JR
authors: Miller
authors: Kevin V
authors: KV
authors: Haub
authors: David J
authors: DJ
authors: Dooling
authors: Elaine R
authors: ER
authors: Mardis
authors: Richard K
authors: RK
authors: Wilson
authors: George M
authors: GM
authors: Weinstock
authors: Wesley C
authors: WC
authors: Warren
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D019295:Computational Biology; D018076:DNA, Complementary; D005260:Female; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics; D011786:Quality Control; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary