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Sequence analysis

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

Martin Laurence, Christos Hatzis, Douglas E. Brash

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

Emma M. Quinn, Paul Cormican, [ ... ], Derek W. Morris

Unlocking Short Read Sequencing for Metagenomics

Sébastien Rodrigue, Arne C. Materna, [ ... ], Sallie W. Chisholm

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

R. Henrik Nilsson, Martin Ryberg, [ ... ], Urmas Kõljalg

The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing

Jonas Binladen, M. Thomas P. Gilbert, [ ... ], Eske Willerslev

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

Jack A. Gilbert, Dawn Field, [ ... ], Ian Joint

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

Rym Fekih, Hiroki Takagi, [ ... ], Ryohei Terauchi

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

Xiangtao Liu, Shizhong Han, [ ... ], Bao-Zhu Yang

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

Brian B. Tuch, Rebecca R. Laborde, [ ... ], David I. Smith

Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions

Jasmin F. Sydow, Florian Lipsmeier, [ ... ], Hubert Kettenberger

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data

Marcelo V. Kitahara, Stephen D. Cairns, [ ... ], David J. Miller

Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment

Alexander Kawrykow, Gary Roumanis, [ ... ], Jérôme Waldispühl

Compression of FASTQ and SAM Format Sequencing Data

James K. Bonfield, Matthew V. Mahoney

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