ARACHNE: a whole-genome shotgun assembler. We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing approximately 10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and D. melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the D. melanogaster genome yielded approximately 98% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of approximately 1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.

References in zbMATH (referenced in 9 articles )

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  1. Wright, Christopher; Krishnamoorty, Sriram; Kulkarni, Milind: MULKSG: \textitMULtiple\textitK\textitSimultaneous\textitGraphassembly (2019)
  2. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  3. Nimmy, Sonia Farhana; Kamal, M. S.: Next generation sequencing under de novo genome assembly (2015)
  4. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  5. Prosperi, Mattia C. F.; Prosperi, Luciano; Bruselles, Alessandro; Abbate, Isabella; Rozera, Gabriella; Vincenti, Donatella; Solmone, Maria Carmela; Capobianchi, Maria Rosaria; Ulivi, Giovanni: Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing (2011) ioport
  6. Kingsford, Carl; Schatz, Michael C.; Pop, Mihai: Assembly complexity of prokaryotic genomes using short reads (2010) ioport
  7. Palmer, Lance E.; Dejori, Mathäus; Bolanos, Randall A.; Fasulo, Daniel P.: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction (2010) ioport
  8. Peto, Myron; Grant, David M.; Shoemaker, Randy C.; Cannon, Steven B.: Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences (2010)
  9. Kim, Jin Wook; Park, Kunsoo: An efficient alignment algorithm for masked sequences (2007)