Indiana University
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Using Phrap/Cross_match/Swat on Big Red

Phrap/Cross_match/Swat is a set of programs for DNA analysis. Phrap (short for "phragment assembly program") assembles shotgun DNA sequence data. Swat searches DNA/protein sequences, or a query profile, against a sequence database. Cross_match compares any two DNA sequence sets. The current version installed on Big Red at Indiana University is 17.0. For more, see the Phrap/Cross_match/Swat section of the Phrap web site.

On this page:

  1. Request a Big Red account
  2. Send an academic user license agreement
  3. Set up SoftEnv and submit jobs

Request a Big Red account

Access to Big Red is provided to all IU faculty and graduate students, and faculty-sponsored undergraduates and staff. Instructional use is limited to courses that have been approved by the Director for Research Technologies. If you use Big Red, you need to know the Big Red usage policies.

To request a Big Red account, use the Account Management System (AMS); see Instructions for getting more computing accounts at IU For more, see Getting started on Big Red.

Send an academic user license agreement

Phrap/Cross_match/Swat is a restricted-use package available only to CAP3 group users. If you are at IU and want to use this software, read the academic user agreement. Then email BIOS noting your agreement to the license terms, asking to use the Phrap/Cross_match/Swat package on Big Red, and providing the information requested on that web page. After UITS staff receive the license agreements, you will be added as a CAP3 group member and will receive an email confirmation.

Set up SoftEnv and submit jobs

  1. To set up your SoftEnv, edit your .soft file to add the line +cross_match and execute the resoft command.

  2. The introduction document file is available at /N/soft/linux-sles9-ppc64/Phrap/bin/cross_match.help.

  3. To see the options for this package, enter phrap/cross_match/swat or see /N/soft/linux-sles9-ppc64/phrap/bin/cross_match.

  4. If your job will run for fewer than 20 minutes, call Phrap/Cross_match/Swat in the directory where your input files are.

    If your program will run for longer than 20 minutes, use the serialjob command. For help, use the man command or see On Big Red at IU, how do I use the serialjob script to submit jobs?

Output that Phrap/Cross_match/Swat generates will be in the same directory as your input files.