Assembly and annotation of an Ashkenazi human reference genome

[1]  Nathan D. Olson,et al.  Assembly and annotation of an Ashkenazi human reference genome , 2020, Genome Biology.

[2]  Aleksey V. Zimin,et al.  The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies , 2019, bioRxiv.

[3]  Sergey Koren,et al.  A robust benchmark for germline structural variant detection , 2019, bioRxiv.

[4]  Simon C. Potter,et al.  The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..

[5]  Birgit Funke,et al.  Best practices for benchmarking germline small-variant calls in human genomes , 2019, Nature Biotechnology.

[6]  Chunlin Xiao,et al.  An open resource for accurately benchmarking small variant and reference calls , 2019, Nature Biotechnology.

[7]  A. Dobin,et al.  Is it time to change the reference genome? , 2019, bioRxiv.

[8]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[9]  Ryan L. Collins,et al.  Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes , 2019, bioRxiv.

[10]  S. Salzberg,et al.  CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise , 2018, Genome Biology.

[11]  Pui-Yan Kwok,et al.  De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations , 2018, Nature Communications.

[12]  Benjamin Neale,et al.  A synthetic-diploid benchmark for accurate variant calling evaluation , 2018, Nature Methods.

[13]  Adam M. Phillippy,et al.  MUMmer4: A fast and versatile genome alignment system , 2018, PLoS Comput. Biol..

[14]  A. Predeus,et al.  Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling , 2017, Genetics in Medicine.

[15]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[16]  S. Fullerton,et al.  Genomics is failing on diversity , 2016, Nature.

[17]  J. Korlach,et al.  De novo assembly and phasing of a Korean human genome , 2016, Nature.

[18]  E. Hendrickson,et al.  Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4 , 2016, Genome research.

[19]  Alexa B. R. McIntyre,et al.  Extensive sequencing of seven human genomes to characterize benchmark reference materials , 2015, Scientific Data.

[20]  John G. Cleary,et al.  Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines , 2015, bioRxiv.

[21]  J. M. Harvey,et al.  The Use of Non-Variant Sites to Improve the Clinical Assessment of Whole-Genome Sequence Data , 2015, PloS one.

[22]  B. Giusti,et al.  Characterization and identification of hidden rare variants in the human genome , 2015, BMC Genomics.

[23]  Madeleine P. Ball,et al.  Harvard Personal Genome Project: lessons from participatory public research , 2014, Genome Medicine.

[24]  J. Zook,et al.  Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls , 2013, Nature Biotechnology.

[25]  Michael Roberts,et al.  The MaSuRCA genome assembler , 2013, Bioinform..

[26]  Glenn Tesler,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

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

[28]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[29]  A. Need,et al.  Next generation disparities in human genomics: concerns and remedies. , 2009, Trends in genetics : TIG.

[30]  J. Murnane,et al.  Telomeres, chromosome instability and cancer , 2006, Nucleic acids research.

[31]  G. Church,et al.  The Personal Genome Project , 2005, Molecular systems biology.

[32]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[33]  J. Murnane,et al.  The DNA damage response at dysfunctional telomeres, and at interstitial and subtelomeric DNA double-strand breaks. , 2018, Genes & genetic systems.

[34]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[35]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[36]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.