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Resource: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- Aaron McKenna,
- Matthew Hanna,
- Eric Banks,
- Andrey Sivachenko,
- Kristian Cibulskis,
- Andrew Kernytsky,
- Kiran Garimella,
- David Altshuler,
- Stacey Gabriel,
- Mark Daly,
- and Mark A. DePristo
Genome Res. September 2010 20: 1297-1303; Published in Advance July 19, 2010, doi:10.1101/gr.107524.110
...P, Pages H, Gentleman R. 2009. ShortRead: A bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25: 2607– 2608. Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: A fast search method for large DNA databases. Genome Res 11: 1725–1729. Pepke S...
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RESOURCE: Mapping short DNA sequencing reads and calling variants using mapping quality scores
- Heng Li,
- Jue Ruan,
- and Richard Durbin
Genome Res. November 2008 18: 1851-1858; Published in Advance August 19, 2008, doi:10.1101/gr.078212.108
...Mapping short DNA sequencing reads and calling variants using mapping quality scores Heng Li 1 , Jue Ruan 2 , and Richard Durbin 1 , 3 1 The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; 2 Beijing Genomics...
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METHODS: Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA
- Thomas A. Down and
- Tim J. P. Hubbard
Genome Res. March 1, 2002 12: 458-461; doi:10.1101/gr.216102
...) Generalized linear models. ( Chapman and Hall , London ). ↵ Ning Z. , Cox A.J. , Mullikin J.C. ( 2001 ) SSAHA: A fast search method for large DNA databases. Genome Res. 11 : 1725 – 1729 . ↵ Perier R.C. , Praz V. , Junier T. , Bonnard C. , Bucher P. ( 2000 ) The eukaryotic promoter database (EPD). Nucleic...
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METHODS: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
- Michael Brudno,
- Chuong B. Do,
- Gregory M. Cooper,
- Michael F. Kim,
- Eugene Davydov,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. April 1, 2003 13: 721-731; Published in Advance March 12, 2003, doi:10.1101/gr.926603
...LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Michael Brudno 1 , Chuong B. Do 1 , Gregory M. Cooper 2 , Michael F. Kim 1 , Eugene Davydov 1 , NISC Comparative Sequencing Program 1...
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Method: Enhanced virome sequencing using targeted sequence capture
- Todd N. Wylie,
- Kristine M. Wylie,
- Brandi N. Herter,
- and Gregory A. Storch
Genome Res. December 2015 25: 1910-1920; Published in Advance September 22, 2015, doi:10.1101/gr.191049.115
...analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into &lt;200 million bp of unique, representative...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
...and thus identified 15,708unique rice nTARs.Of the 15,708unique nTARs, 8126 (51.7%) found no hits in public protein databases when searching against NCBI nrDB (E-value# 13 10#2;6). Only 713 nTARs of the 8126 were predicted open reading frames with >100 amino acids (aa). Of the 7582 matched nTARs, 3718 n...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
....L. 1997 . Polyphred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25 : 2745 –2751. ↵ Ning, Z., Cox, A.J., and Mullikin, J.C. 2001 . SSAHA: A fast search method for large DNA databases. Genome Res. 11 : 1725 –1729...
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Resource: An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
- Rosaria Scozzari,
- Andrea Massaia,
- Beniamino Trombetta,
- Giovanna Bellusci,
- Natalie M. Myres,
- Andrea Novelletto,
- and Fulvio Cruciani
Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113
...involvedwhen using a sequence that is mainly derived from haplogroup P DNA as a reference, and to the intense sequencing and search for mutations carried out on haplogroup P subjects (Underhill et al. 2010; Myres et al. 2011). In order to further confirm the increase in branch length compared with previous...
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Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
- Sergey Koren,
- Brian P. Walenz,
- Konstantin Berlin,
- Jason R. Miller,
- Nicholas H. Bergman,
- and Adam M. Phillippy
Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
...). Canu stages share an interface for binary ondisk stores (databases), as well as parallel store construction. In all stages, the first step constructs an indexed store of input sequences, generates a k-mer histogram, constructs an indexed store of all-versus-all overlaps, and collates summary statistics...
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Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
.... Nucleic Acids Res 35: e97. doi: 10.1093/nar/gkm566. Moriyama EN, Powell JR. 1996. Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13: 261–277. Mullikin JC, Ning Z. 2003. The Phusion assembler. Genome Res 13: 81–90. Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: A fast search method for large...

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