Publications by authors named "Erik Garrison"

27Publications

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.

Genome Biol 2020 09 17;21(1):250. Epub 2020 Sep 17.

Department of Genetics, University of Cambridge, Cambridge, CB3 0DH, UK.

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http://dx.doi.org/10.1186/s13059-020-02160-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499850PMC
September 2020

Pangenome Graphs.

Annu Rev Genomics Hum Genet 2020 Aug 26;21:139-162. Epub 2020 May 26.

Genomics Institute, University of California, Santa Cruz, California 95064, USA; email:

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http://dx.doi.org/10.1146/annurev-genom-120219-080406DOI Listing
August 2020

Genotyping structural variants in pangenome graphs using the vg toolkit.

Genome Biol 2020 02 12;21(1):35. Epub 2020 Feb 12.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA.

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http://dx.doi.org/10.1186/s13059-020-1941-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017486PMC
February 2020

Haplotype-aware graph indexes.

Bioinformatics 2020 01;36(2):400-407

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223266PMC
January 2020

A graph-based approach to diploid genome assembly.

Bioinformatics 2018 07;34(13):i105-i114

Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany.

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https://academic.oup.com/bioinformatics/article/34/13/i105/5
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http://dx.doi.org/10.1093/bioinformatics/bty279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022571PMC
July 2018

Superbubbles, Ultrabubbles, and Cacti.

J Comput Biol 2018 07 20;25(7):649-663. Epub 2018 Feb 20.

1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California.

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http://www.liebertpub.com/doi/10.1089/cmb.2017.0251
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http://dx.doi.org/10.1089/cmb.2017.0251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067107PMC
July 2018

A graph extension of the positional Burrows-Wheeler transform and its applications.

Algorithms Mol Biol 2017 11;12:18. Epub 2017 Jul 11.

Genomics Institute, University of California Santa Cruz, CBSE, 501C Engineering 2, MS: CBSE, 1156 High St., Santa Cruz, CA 95064 USA.

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http://dx.doi.org/10.1186/s13015-017-0109-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505026PMC
July 2017

Genome graphs and the evolution of genome inference.

Genome Res 2017 05 30;27(5):665-676. Epub 2017 Mar 30.

Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1101/gr.214155.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762PMC
May 2017

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Nat Methods 2015 Oct 10;12(10):966-8. Epub 2015 Aug 10.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nmeth.3505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589466PMC
October 2015

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PLoS One 2014 5;9(3):e90581. Epub 2014 Mar 5.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944147PMC
January 2015

SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

PLoS One 2013 4;8(12):e82138. Epub 2013 Dec 4.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082138PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852983PMC
September 2014

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Bioinformatics 2011 Jun 14;27(12):1691-2. Epub 2011 Apr 14.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106182PMC
June 2011