eagle-i Oregon Health & Science UniversityOregon Health & Science University
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Consed: a graphical tool for sequence finishing.

eagle-i ID

http://ohsu.eagle-i.net/i/0000012f-7e9a-6054-fb77-395980000000

Resource Type

  1. Journal article

Properties

  1. Resource Description
    "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."
  2. Website(s)
    http://www.ncbi.nlm.nih.gov/pubmed/9521923?dopt=Abstract&holding=npg
  3. PubMed ID
    9521923
 
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Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016