Assembling Genomic DNA Sequences with PHRAP

Melissa de la Bastide1, W. Richard McCombie1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.4
DOI:  10.1002/0471250953.bi1104s17
Online Posting Date:  March, 2007
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

The PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet certain criteria. If a match is found, PHRAP then tries to extend the alignment into overlapping sections called contigs. PHRAP uses quality values produced by the PHRED basecaller to strike a balance between tolerance of discrepancies and prevention of stacking repeat sequences. The PHRAP assembly algorithm is generally used as part of the PHRED/PHRAP/Consed software suite for sequence analysis. This unit presents instructions for basic usage of the PHRAP assembler, including preparation of the input files (Support Protocols 1 and 2) and explanation of output files (Basic Protocols 1 and 2). Several command line options for changing the PHRAP assembly parameters are also discussed (Basic Protocol 3).

Keywords: PHRAP; sequence assembly; DNA

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Basic Protocol 1: Generating a PHRAP Assembly Using the Stand‐Alone Version of PHRAP on an Example Data Set
  • Basic Protocol 2: Generating an Assembly Using the phredPhrap Script on an Example Data Set
  • Basic Protocol 3: Changing Assembly Parameters
  • Support Protocol 1: Input Files
  • Support Protocol 2: Read Naming Conventions
  • Commentary
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

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. 1998. 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.
   Gotoh, O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162:705‐708.
   Smith, T.F. and Waterman, M.S. 1981. Identication of common molecular subsequences. J. Mol. Biol. 147:195‐197.
Internet Resources
  http://bozeman.mbt.washington.edu
   Green, P. 1996. Documentation for PHRAP. Genome Center, University of Washington, Seattle.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library