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      Consed: a graphical tool for sequence finishing.

      1 , ,
      Genome research
      Cold Spring Harbor Laboratory

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          Abstract

          Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred and phrap as an objective criterion to guide the entire finishing process. More information is available at http:// www.genome.washington.edu/consed/consed. html.

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          Author and article information

          Journal
          Genome Res
          Genome research
          Cold Spring Harbor Laboratory
          1088-9051
          1088-9051
          Mar 1998
          : 8
          : 3
          Affiliations
          [1 ] Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730, USA. gordon@genome.washington.edu
          Article
          10.1101/gr.8.3.195
          9521923
          2b766dcc-d9e6-426d-addb-f269c1eff54b
          History

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