Searching journal content for articles similar to Lunter and Goodson 21 (6): 936.

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  1. Method: Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
    • Nicholas J. Parkinson,
    • Siarhei Maslau,
    • Ben Ferneyhough,
    • Gang Zhang,
    • Lorna Gregory,
    • David Buck,
    • Jiannis Ragoussis,
    • Chris P. Ponting,
    • and Michael D. Fischer
    Genome Res. January 2012 22: 125-133; Published in Advance November 16, 2011, doi:10.1101/gr.124016.111
    ...immediately Table 1. Quality statistics for 1-mg Illumina and 10-pg-level tagmented libraries Target DNA E. coli gDNA Method Illumina Tagmentation AcuI BsgI/BpmI Blended from all four DNA input 1 mg 10 pg 23 10 pg 43 10 pg Demultiplexed reads >phred 20 3,932,654 (100%) 4,125,988 (100%) 4,684,314 (100%) 3...
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  2. Resource: Dindel: Accurate indel calls from short-read data
    • Cornelis A. Albers,
    • Gerton Lunter,
    • Daniel G. MacArthur,
    • Gilean McVean,
    • Willem H. Ouwehand,
    • and Richard Durbin
    Genome Res. June 2011 21: 961-973; Published in Advance October 27, 2010, doi:10.1101/gr.112326.110
    ...indel model for Illumina reads and were not designed for analyzing pools of samples. To the best of our knowledge, our method is the first to address the realignment problem and various sources of errors explicitly in a single statistical framework, in particular the modeling of context...
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  3. Method: Genome assembly quality: Assessment and improvement using the neutral indel model
    • Stephen Meader,
    • LaDeana W. Hillier,
    • Devin Locke,
    • Chris P. Ponting,
    • and Gerton Lunter
    Genome Res. May 2010 20: 675-684; Published in Advance March 19, 2010, doi:10.1101/gr.096966.109
    ...is lower at approximately fourfold (Orangutan Genome Sequencing Consortium, in prep.). We were able to take advantage of a data set of short reads at approximately 10-fold statistical coverage from a single Bornean orangutan (Pongo pygmaeus pygmaeus) thatwas shotgun-sequenced using the Illumina short read...
  4. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    .... The sequencing was done with Illumina HiSeq 2000 or NovaSeq 6000 by the NGS platform of the University of Bern. Raw reads of all individuals (Fig. 1A; Supplemental Table S1) were mapped to the reference of M. arvalis (BioProject ID: PRJNA737461; A Gouy, X Wang, A Kapopoulou, et al., in prep.) using Stampy 1...
  5. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...Indian state of Himachal Pradesh (Halligan et al. 2010, 2013). Reads were mapped against mouse mm9 using BWA (Li and Durbin 2009) and Stampy (Lunter and Goodson 2011). As coding regions in mm9 are well annotated, use of more recent builds would not affect our conclusions. Duplicate reads were marked...
  6. Research: Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
    • Neel Prabh,
    • Waltraud Roeseler,
    • Hanh Witte,
    • Gabi Eberhardt,
    • Ralf J. Sommer,
    • and Christian Rödelsperger
    Genome Res. November 2018 28: 1664-1674; Published in Advance September 19, 2018, doi:10.1101/gr.234971.118
    ...M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21: 936–939. ↵Lynch M. 2007. The origins of architecture. Sinauer Associates, Inc., Sunderland, MA. ↵MacCallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, Mc...
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  7. Research: Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
    • Pille Hallast,
    • Pierpaolo Maisano Delser,
    • Chiara Batini,
    • Daniel Zadik,
    • Mariano Rocchi,
    • Werner Schempp,
    • Chris Tyler-Smith,
    • and Mark A. Jobling
    Genome Res. April 2016 26: 427-439; Published in Advance February 16, 2016, doi:10.1101/gr.198754.115
    .... This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping...
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  8. Research: Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
    • Hongru Wang,
    • Filipe G. Vieira,
    • Jacob E. Crawford,
    • Chengcai Chu,
    • and Rasmus Nielsen
    Genome Res. June 2017 27: 1029-1038; Published in Advance April 6, 2017, doi:10.1101/gr.204800.116
    ...), and the mapping was further improved with Stampy (version 1.0.20) (Lunter and Goodson 2011). PCR duplicates were removed by “rmdup” in SAMtools (version 0.17) (Li et al. 2009). We realigned reads at gapped regions with GATK (version 2.6) (DePristo et al. 2011). Population structure, phylogeny, network, and Tree...
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  9. Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
    • Yang I. Li,
    • Luis Sanchez-Pulido,
    • Wilfried Haerty,
    • and Chris P. Ponting
    Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
    ...prefrontal cortices (Lonsdale et al. 2013), and 531 samples from diverse human and mouse tissues (Merkin et al. 2012; Lonsdale et al. 2013); Illumina Human BodyMap Project (European Nucleotide Archive [ENA; http://www.ebi.ac.uk/ena/]; accession number ERA022994) to show that thousands of micro...
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  10. Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
    • Simon H. Martin,
    • Kanchon K. Dasmahapatra,
    • Nicola J. Nadeau,
    • Camilo Salazar,
    • James R. Walters,
    • Fraser Simpson,
    • Mark Blaxter,
    • Andrea Manica,
    • James Mallet,
    • and Chris D. Jiggins
    Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
    ...to the manufacturer’s protocol (Illumina Inc.). These were shotgun sequenced on either Illumina’s Genome Analyzer IIx system or Illumina’s HiSeq 2000 system, according to the manufacturer’s protocol (Illumina Inc.). Quality-filtered, paired-end sequence reads were mapped to the H. melpomene scaffolds (version 1...
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