Genome Biology

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Accuracy and quality of massively parallel DNA pyrosequencing

Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin* and David M Welch

Genome Biology 2007, 8:R143 doi:10.1186/gb-2007-8-7-r143

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BioMed Central: 29 citations

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GemSIM: general, error-model based simulator of next-generation sequencing data

Kerensa E McElroy, Fabio Luciani, Torsten Thomas BMC Genomics 2012, 13:74 (15 February 2012)

Research article   Open Access Highly Accessed

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

Monica F Poelchau, Julie A Reynolds, David L Denlinger, Christine G Elsik, Peter A Armbruster BMC Genomics 2011, 12:619 (20 December 2011)

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Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

Jorge Barriuso, Jose R Valverde , Rafael P Mellado BMC Bioinformatics 2011, 12:473 (14 December 2011)

Review   Open Access

Molecular musings in microbial ecology and evolution

Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011)

This article is part of a collection on Beyond the tree of life

Technical Note   Open Access

An efficient simulator of 454 data using configurable statistical models

Fredrik Lysholm, Björn Andersson, Bengt Persson BMC Research Notes 2011, 4:449 (26 October 2011)

Research   Open Access

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

Athanasia C Tzika, Raphaël Helaers, Gerrit Schramm, Michel C Milinkovitch EvoDevo 2011, 2:19 (26 September 2011)

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SAMQA: error classification and validation of high-throughput sequenced read data

Thomas Robinson, Sarah Killcoyne, Ryan Bressler, John Boyle BMC Genomics 2011, 12:419 (18 August 2011)

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Metagenomic biomarker discovery and explanation

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower Genome Biology 2011, 12:R60 (24 June 2011)

A method for distinguishing microbial populations from metagenomic data is presented

Research   Open Access

Filtering "genic" open reading frames from genomic DNA samples for advanced annotation

Sara D'Angelo, Nileena Velappan, Flavio Mignone, Claudio Santoro, Daniele Sblattero, Csaba Kiss, Andrew RM Bradbury BMC Genomics 2011, 12(Suppl 1):S5 (15 June 2011)

Software   Open Access

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

Robert Schmieder, Yan Lim, Forest Rohwer, Robert Edwards BMC Bioinformatics 2010, 11:341 (23 June 2010)

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SNP identification, verification, and utility for population genetics in a non-model genus

Larissa M Williams, Xin Ma, Adam R Boyko, Carlos D Bustamante, Marjorie F Oleksiak BMC Genetics 2010, 11:32 (30 April 2010)

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Artificial and natural duplicates in pyrosequencing reads of metagenomic data

Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li BMC Bioinformatics 2010, 11:187 (13 April 2010)

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Environmental distribution of prokaryotic taxa

Javier Tamames, Juan Abellán, Miguel Pignatelli, Antonio Camacho, Andrés Moya BMC Microbiology 2010, 10:85 (22 March 2010)

This article is part of a collection on Open Access Biodiversity...

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Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

Thomas L Parchman, Katherine S Geist, Johan A Grahnen, Craig W Benkman, C Alex Buerkle BMC Genomics 2010, 11:180 (16 March 2010)

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The effect of sequencing errors on metagenomic gene prediction

Katharina J Hoff BMC Genomics 2009, 10:520 (12 November 2009)

Research article   Open Access

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Thorsten Stoeck, Anke Behnke, Richard Christen, Linda Amaral-Zettler, Maria J Rodriguez-Mora, Andrei Chistoserdov, William Orsi, Virginia P Edgcomb BMC Biology 2009, 7:72 (3 November 2009)

This article is part of a collection on Open Access Biodiversity...

High-throughput parallel tag sequencing combined with a novel bioinformatic pipeline detects a rich diversity of protists in two contrasting anoxic marine environments, finding many taxon groups missed by previous clone-based surveys.

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Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing

Wei Wang, Yejun Wang, Qing Zhang, Yan Qi, Dianjing Guo BMC Genomics 2009, 10:465 (9 October 2009)

Method   Open Access Highly Accessed

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009)

A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data

Research   Open Access

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Eeva M Soininen, Alice Valentini, Eric Coissac, Christian Miquel, Ludovic Gielly, Christian Brochmann, Anne K Brysting, Jørn H Sønstebø, Rolf A Ims, Nigel G Yoccoz, Pierre Taberlet Frontiers in Zoology 2009, 6:16 (20 August 2009)

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Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Erik Kristiansson, Noomi Asker, Lars Förlin, DG Joakim Larsson BMC Genomics 2009, 10:345 (31 July 2009)

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Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

Daniel A Hahn, Gregory J Ragland, D Shoemaker, David L Denlinger BMC Genomics 2009, 10:234 (19 May 2009)

A large number of ESTs and microsatellite markers have been obtained by massively parallel pyrosequencing in the flesh fly S. crassipalpis, an important insect model for physiology and biochemistry

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PanGEA: Identification of allele specific gene expression using the 454 technology

Robert Kofler, Tatiana Teixeira Torres, Tamas Lelley, Christian Schlötterer BMC Bioinformatics 2009, 10:143 (14 May 2009)

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A transcriptional sketch of a primary human breast cancer by 454 deep sequencing

Alessandro Guffanti, Michele Iacono, Paride Pelucchi, Namshin Kim, Giulia Soldà, Larry J Croft, Ryan J Taft, Ermanno Rizzi, Marjan Askarian-Amiri, Raoul J Bonnal, Maurizio Callari, Flavio Mignone, Graziano Pesole, Giovanni Bertalot, Luigi Bernardi, Alberto Albertini, Christopher Lee, John S Mattick, Ileana Zucchi, Gianluca De Bellis BMC Genomics 2009, 10:163 (20 April 2009)

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Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

Gabriella Rozera, Isabella Abbate, Alessandro Bruselles, Crhysoula Vlassi, Gianpiero D'Offizi, Pasquale Narciso, Giovanni Chillemi, Mattia Prosperi, Giuseppe Ippolito, Maria R Capobianchi Retrovirology 2009, 6:15 (12 February 2009)

Technical Note   Open Access

PeakSeeker: a program for interpreting genotypes of mononucleotide repeats

James M Thompson, Stephen J Salipante BMC Research Notes 2009, 2:17 (3 February 2009)

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High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

Jean-Marc Aury, Corinne Cruaud, Valérie Barbe, Odile Rogier, Sophie Mangenot, Gaelle Samson, Julie Poulain, Véronique Anthouard, Claude Scarpelli, François Artiguenave, Patrick Wincker BMC Genomics 2008, 9:603 (16 December 2008)

By combining 454 GSFLX and Solexa-Illumina technologies to sequence medically important microbes, quality is maintained while lowering the cost and time taken to sequence whole genomes.

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The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards BMC Bioinformatics 2008, 9:386 (19 September 2008)

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Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

Scot E Dowd, Todd R Callaway, Randall D Wolcott, Yan Sun, Trevor McKeehan, Robert G Hagevoort, Thomas S Edrington BMC Microbiology 2008, 8:125 (24 July 2008)

Software   Open Access

Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm

Jeremy D DeBarry, Renyi Liu, Jeffrey L Bennetzen BMC Bioinformatics 2008, 9:235 (13 May 2008)