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Genome sequencing

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

Alison F. Feder, Dmitri A. Petrov, Alan O. Bergland

A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing

Martina Mijušković, Stuart M. Brown, [ ... ], David B. Roth

COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

Neeraja M. Krishnan, Prakhar Gaur, [ ... ], Binay Panda

Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data

Zhong Zhuang, Alexander Gusev, Judy Cho, Itsik Pe'er

Improving PacBio Long Read Accuracy by Short Read Alignment

Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong

Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

Fei Yao, Pramila N. Ariyaratne, [ ... ], Yijun Ruan

Paired-End Sequencing of Long-Range DNA Fragments for De Novo Assembly of Large, Complex Mammalian Genomes by Direct Intra-Molecule Ligation

Asan, Chunyu Geng, [ ... ], Xiuqing Zhang

Prolonged and Substantial Discordance in Prevalence of Raltegravir-Resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 “Deep” Sequencing

Guinevere Q. Lee, Luke C. Swenson, [ ... ], P. Richard Harrigan

SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

Elhan S. Ersoz, Mark H. Wright, [ ... ], Denise E. Costich

In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer

Deanna Lee, Jaydip Das Gupta, [ ... ], Charles Y. Chiu

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

Andrew Tritt, Jonathan A. Eisen, Marc T. Facciotti, Aaron E. Darling

Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach

Dean B. Everett, Jennifer Cornick, [ ... ], Stephen D. Bentley

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Colin F. Davenport, Jens Neugebauer, [ ... ], Frauke Sprengel

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