ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

[1]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[2]  Rhys A. Farrer,et al.  De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. , 2009, FEMS microbiology letters.

[3]  Richard Durbin,et al.  A large genome center's improvements to the Illumina sequencing system , 2008, Nature Methods.

[4]  Eric S. Lander,et al.  Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing , 2008, Nature Methods.

[5]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[6]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[7]  David Hernández,et al.  De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[8]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[9]  S. Quake,et al.  Single-Molecule DNA Sequencing of a Viral Genome , 2008, Science.

[10]  Mark J. P. Chaisson,et al.  Short read fragment assembly of bacterial genomes. , 2008, Genome research.

[11]  Juliane C. Dohm,et al.  SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.

[12]  Vincent J. Magrini,et al.  Extending assembly of short DNA sequences to handle error , 2007, Bioinform..

[13]  René L. Warren,et al.  Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..

[14]  R. Service.  The Race for the $1000 Genome , 2006, Science.

[15]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[16]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[17]  R. Myers,et al.  Quality assessment of the human genome sequence , 2004, Nature.

[18]  E. Mauceli,et al.  The genome sequence of the filamentous fungus Neurospora crassa , 2003, Nature.

[19]  Mihai Pop,et al.  Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis , 2002, Science.

[20]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[21]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[22]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[23]  F. Collins,et al.  Directional cloning of DNA fragments at a large distance from an initial probe: a circularization method. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Mark J. P. Chaisson,et al.  De novo fragment assembly with short mate-paired reads: Does the read length matter? , 2009, Genome research.

[25]  System Mate-Paired Libraries Detect and Define Large Genetic Rearrangements , 2008 .