UNIT 11.4 Assembling Genomic DNA Sequences with PHRAP

  1. Melissa de la Bastide,
  2. W. Richard McCombie

Published Online: 1 MAR 2007

DOI: 10.1002/0471250953.bi1104s17

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

de la Bastide, M. and McCombie, W. R. 2007. Assembling Genomic DNA Sequences with PHRAP. Current Protocols in Bioinformatics. 17:11.4:11.4.1–11.4.15.

Author Information

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

Publication History

  1. Published Online: 1 MAR 2007
  2. Published Print: MAR 2007


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).


  • PHRAP;
  • sequence assembly;
  • DNA