Literature DB >> 23065605

Library preparation and data analysis packages for rapid genome sequencing.

Kyle R Pomraning1, Kristina M Smith, Erin L Bredeweg, Lanelle R Connolly, Pallavi A Phatale, Michael Freitag.   

Abstract

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.

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Year:  2012        PMID： 23065605      PMCID： PMC3686501          DOI： 10.1007/978-1-62703-122-6_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  37 in total

1.  Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1.

Authors:  Kyle R Pomraning; Kristina M Smith; Michael Freitag
Journal:  Eukaryot Cell       Date:  2011-04-22

2.  Comparative studies of de novo assembly tools for next-generation sequencing technologies.

Authors:  Yong Lin; Jian Li; Hui Shen; Lei Zhang; Christopher J Papasian; Hong-Wen Deng
Journal:  Bioinformatics       Date:  2011-06-02       Impact factor: 6.937

3.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

Authors:  Gerton Lunter; Martin Goodson
Journal:  Genome Res       Date:  2010-10-27       Impact factor: 9.043

4.  De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.

Authors:  Josephine A Reinhardt; David A Baltrus; Marc T Nishimura; William R Jeck; Corbin D Jones; Jeffery L Dangl
Journal:  Genome Res       Date:  2008-11-17       Impact factor: 9.043

5.  SOAP: short oligonucleotide alignment program.

Authors:  Ruiqiang Li; Yingrui Li; Karsten Kristiansen; Jun Wang
Journal:  Bioinformatics       Date:  2008-01-28       Impact factor: 6.937

6.  Identifying dispersed epigenomic domains from ChIP-Seq data.

Authors:  Qiang Song; Andrew D Smith
Journal:  Bioinformatics       Date:  2011-02-16       Impact factor: 6.937

7.  GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Authors:  Jason S Cumbie; Jeffrey A Kimbrel; Yanming Di; Daniel W Schafer; Larry J Wilhelm; Samuel E Fox; Christopher M Sullivan; Aron D Curzon; James C Carrington; Todd C Mockler; Jeff H Chang
Journal:  PLoS One       Date:  2011-10-06       Impact factor: 3.240

8.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Authors:  Daniel Aird; Michael G Ross; Wei-Sheng Chen; Maxwell Danielsson; Timothy Fennell; Carsten Russ; David B Jaffe; Chad Nusbaum; Andreas Gnirke
Journal:  Genome Biol       Date:  2011-02-21       Impact factor: 13.583

9.  FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Authors:  Darshan Singh; Christian F Orellana; Yin Hu; Corbin D Jones; Yufeng Liu; Derek Y Chiang; Jinze Liu; Jan F Prins
Journal:  Bioinformatics       Date:  2011-08-08       Impact factor: 6.937

10.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583
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  11 in total

1.  Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

Authors:  Jessica L Soyer; Mareike Möller; Klaas Schotanus; Lanelle R Connolly; Jonathan M Galazka; Michael Freitag; Eva H Stukenbrock
Journal:  Fungal Genet Biol       Date:  2015-04-07       Impact factor: 3.495

2.  Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.

Authors:  Philipp Wiemann; Christian M K Sieber; Katharina W von Bargen; Lena Studt; Eva-Maria Niehaus; Jose J Espino; Kathleen Huß; Caroline B Michielse; Sabine Albermann; Dominik Wagner; Sonja V Bergner; Lanelle R Connolly; Andreas Fischer; Gunter Reuter; Karin Kleigrewe; Till Bald; Brenda D Wingfield; Ron Ophir; Stanley Freeman; Michael Hippler; Kristina M Smith; Daren W Brown; Robert H Proctor; Martin Münsterkötter; Michael Freitag; Hans-Ulrich Humpf; Ulrich Güldener; Bettina Tudzynski
Journal:  PLoS Pathog       Date:  2013-06-27       Impact factor: 6.823

3.  Two histone deacetylases, FfHda1 and FfHda2, are important for Fusarium fujikuroi secondary metabolism and virulence.

Authors:  L Studt; F J Schmidt; L Jahn; C M K Sieber; L R Connolly; E-M Niehaus; M Freitag; H-U Humpf; B Tudzynski
Journal:  Appl Environ Microbiol       Date:  2013-10-04       Impact factor: 4.792

4.  Transcriptome characterization by RNA-Seq reveals the involvement of the complement components in noise-traumatized rat cochleae.

Authors:  M Patel; Z Hu; J Bard; J Jamison; Q Cai; B H Hu
Journal:  Neuroscience       Date:  2013-05-30       Impact factor: 3.590

5.  Neurospora importin α is required for normal heterochromatic formation and DNA methylation.

Authors:  Andrew D Klocko; Michael R Rountree; Paula L Grisafi; Shan M Hays; Keyur K Adhvaryu; Eric U Selker
Journal:  PLoS Genet       Date:  2015-03-20       Impact factor: 5.917

6.  Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes.

Authors:  Klaas Schotanus; Jessica L Soyer; Lanelle R Connolly; Jonathan Grandaubert; Petra Happel; Kristina M Smith; Michael Freitag; Eva H Stukenbrock
Journal:  Epigenetics Chromatin       Date:  2015-10-01       Impact factor: 4.954

7.  The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters.

Authors:  Lanelle R Connolly; Kristina M Smith; Michael Freitag
Journal:  PLoS Genet       Date:  2013-10-31       Impact factor: 5.917

8.  Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes.

Authors:  Sen Wang; Jiedan Chen; Wenpan Zhang; Yan Hu; Lijing Chang; Lei Fang; Qiong Wang; Fenni Lv; Huaitong Wu; Zhanfeng Si; Shuqi Chen; Caiping Cai; Xiefei Zhu; Baoliang Zhou; Wangzhen Guo; Tianzhen Zhang
Journal:  Genome Biol       Date:  2015-05-24       Impact factor: 13.583

9.  The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion.

Authors:  Rigzin Dekhang; Cheng Wu; Kristina M Smith; Teresa M Lamb; Matthew Peterson; Erin L Bredeweg; Oneida Ibarra; Jillian M Emerson; Nirmala Karunarathna; Anna Lyubetskaya; Elham Azizi; Jennifer M Hurley; Jay C Dunlap; James E Galagan; Michael Freitag; Matthew S Sachs; Deborah Bell-Pedersen
Journal:  G3 (Bethesda)       Date:  2017-01-05       Impact factor: 3.154

10.  Functional analyses of Trichoderma reesei LAE1 reveal conserved and contrasting roles of this regulator.

Authors:  Razieh Karimi-Aghcheh; Jin Woo Bok; Pallavi A Phatale; Kristina M Smith; Scott E Baker; Alexander Lichius; Markus Omann; Susanne Zeilinger; Bernhard Seiboth; Catherine Rhee; Nancy P Keller; Michael Freitag; Christian P Kubicek
Journal:  G3 (Bethesda)       Date:  2013-02-01       Impact factor: 3.154
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