Positional bias in variant calls against draft reference assemblies

[1]  Insuk Lee,et al.  Systematic comparison of variant calling pipelines using gold standard personal exome variants , 2015, Scientific Reports.

[2]  Chittibabu Guda,et al.  A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference , 2015, BioMed research international.

[3]  Bjarni V. Halldórsson,et al.  Large-scale whole-genome sequencing of the Icelandic population , 2015, Nature Genetics.

[4]  J. Zook,et al.  An analytical framework for optimizing variant discovery from personal genomes , 2015, Nature Communications.

[5]  R. Schlapbach,et al.  The draft genome of Primula veris yields insights into the molecular basis of heterostyly , 2015, Genome Biology.

[6]  Roberto Solis-Oba,et al.  SAGE: String-overlap Assembly of GEnomes , 2014, BMC Bioinformatics.

[7]  B. Koop,et al.  The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei , 2014, PloS one.

[8]  Heng Li,et al.  Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..

[9]  Arndt von Haeseler,et al.  NextGenMap: fast and accurate read mapping in highly polymorphic genomes , 2013, Bioinform..

[10]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[11]  Safiullah M. Pathan,et al.  Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing , 2013, Proceedings of the National Academy of Sciences.

[12]  Peter Tiffin,et al.  Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula , 2013, PloS one.

[13]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[14]  Matthew D. Schultz,et al.  Patterns of Population Epigenomic Diversity , 2013, Nature.

[15]  Inanç Birol,et al.  Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.

[16]  David W. Cheung,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[17]  Thomas S. Brettin,et al.  The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation , 2012, PloS one.

[18]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[19]  Peter J. Bradbury,et al.  Maize HapMap2 identifies extant variation from a genome in flux , 2012, Nature Genetics.

[20]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[21]  R. Durbin,et al.  Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.

[22]  Andreas Wagner,et al.  The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata , 2012, Mobile DNA.

[23]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[24]  Ümit V. Çatalyürek,et al.  Benchmarking short sequence mapping tools , 2013, BMC Bioinformatics.

[25]  Nuno A. Fonseca,et al.  Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.

[26]  Isaac Y. Ho,et al.  Meraculous: De Novo Genome Assembly with Short Paired-End Reads , 2011, PloS one.

[27]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[28]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[29]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[30]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[31]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[32]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[33]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[34]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[35]  Eugene W. Myers,et al.  The fragment assembly string graph , 2005, ECCB/JBI.

[36]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Lander,et al.  Genomic mapping by fingerprinting random clones: a mathematical analysis. , 1988, Genomics.

[38]  W. Cresko,et al.  Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. , 2012, Methods in molecular biology.

[39]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..