Viewing and Editing Assembled Sequences Using Consed

David Gordon1

1 Howard Hughes Medical Institute, University of Washington, Seattle, Washington
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.2
DOI:  10.1002/0471250953.bi1102s02
Online Posting Date:  August, 2003
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Abstract

Consed is a program for viewing and editing assemblies prepared by the Phrap assembly program. This unit presents a general introduction to Consed. It also provides instructions for identifying problem regions and searching in Consed. Additional protocols describe creating tags, picking primers, correcting joins and adding and removing reads. Instructions are also given for the use of Assembly View, predicting the results of a restriction digestion, the use of Consed in conjunction with PolyPhred, and using Autofinish, as well as a procedure for running Phred and Phrap.

     
 
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Table of Contents

  • Basic Protocol 1: General Introduction to Consed Features
  • Basic Protocol 2: Identifying Problematic Regions in Consed
  • Basic Protocol 3: Creating Tags
  • Basic Protocol 4: Using Consed to Pick Primers
  • Support Protocol 1: Running Phred and Phrap
  • Basic Protocol 5: Tearing and Joining Contigs and Adding and Removing Reads
  • Basic Protocol 6: Assembly View and Miniassemblies
  • Basic Protocol 7: Restriction Digests
  • Basic Protocol 8: Consed‐Polyphred Interaction
  • Basic Protocol 9: Autofinish
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: General Introduction to Consed Features

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB of memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Consed uses the files created by phredPhrap (see protocol 5). However, the files for the example given below are included in the Consed package, and have already been processed by phredPhrap.

Basic Protocol 2: Identifying Problematic Regions in Consed

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: The user must first complete the general introduction (see protocol 1) prior to performing this protocol.

Basic Protocol 3: Creating Tags

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain and install Consed,, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: The user must first complete the general introduction (see protocol 1) prior to performing this protocol.

Basic Protocol 4: Using Consed to Pick Primers

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: Before performing this protocol, the user should first complete the general introduction (see protocol 1), the procedure for identifying problematic regions in Consed (see protocol 2), and the procedure for creating tags (see protocol 3).

Support Protocol 1: Running Phred and Phrap

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Consed uses the files created by phredPhrap. However, the files for the example given below are included in the Consed package, and have already been processed by phredPhrap.NOTE: To perform this protocol, the user will need to have first completed the general introduction (see protocol 1).

Basic Protocol 5: Tearing and Joining Contigs and Adding and Removing Reads

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: The user must first complete the general introduction (see protocol 1) and the procedure for running Phred and Phrap (see protocol 5) prior to performing this protocol.

Basic Protocol 6: Assembly View and Miniassemblies

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAM
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files are included in the Consed packageNOTE: To perform this protocol, the user will need to have first completed the general introduction (see protocol 1), running phredPhrap (see protocol 5), and tearing and joining contigs as well as adding and removing reads (see protocol 6).

Basic Protocol 7: Restriction Digests

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Consed uses the files created by phredPhrap (see protocol 5). However, the files for the example given below are included in the Consed package, and have already been processed by phredPhrap.NOTE: To perform this protocol, the user must first complete the general introduction to Consed's features (see protocol 1).

Basic Protocol 8: Consed‐Polyphred Interaction

  Necessary Resources
      Hardware
  • Workstation with 1 GB RAMAccording to PolyPhred's authors, PolyPhred requires more memory than Consed. They use computers with 1GB RAM for both PolyPhred and Consed projects with ∼200 reads. However, to do this exercise, even 64 MB RAM is adequate.
      Software
  • Consed (http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How To Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: The user must first complete the general introduction (see protocol 1) prior to performing this protocol.

Basic Protocol 9: Autofinish

  Necessary Resources
      Hardware
  • Workstation with ∼256 MB RAMConsed/Autofinish requires ∼256 MB memory for most BACs. Larger projects (or projects with higher depth of coverage) require more memory. See http://www.phrap.org and click Consed and Autofinish for detailed requirements.
      Software
  • Autofinish (included in Consed; http://www.phrap.org)To obtain a Consed license and install it, see http://www.phrap.org and click How to Get Phred/Phrap/Consed. As of this writing, Consed is free to academic users; for commercial users, the Phred/Phrap/Consed package costs about $10,000 per site. See INSTALLING CONSED in README.txt in the Consed package.
      Files
  • Files for the example given below are included in the Consed packageNOTE: The user must first complete the general introduction (see protocol 1) prior to performing this protocol.
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Figures

Videos

Literature Cited

   Ewing, B. and Green, P. 1998. Basecalling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186‐194.
   Ewing, B., Hillier, L., Wendl, M., and Green, P. 1998a. Basecalling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175‐185.
   Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8:195‐202
   Gordon, D., Abajian, C., and Green, P. 2001. Automated finishing with autofinish. Genome Res. 11:614‐625.
Key References
   Ewing and Green, 1998. See above.
  This paper describes Phred.
   Ewing et al., 1998. See above.
  This paper also described Phred.
   Gordon et al., 1998. See above.
  This is the original Consed paper.
   Gordon et al., 2001. See above.
  This paper describes Autofinish.
Internet Resources
   http://www.phrap.org
  The Phred/Phrap/Consed System Home Page
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