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This does mean that breseq is not suited for diploids, and other very large genomes. GATK is a much larger pipeline that has many more additional options. While a tutorial for it can be found here, and students working with human data have still had positive feedback about the remainder of this tutorial.
Bacteriophage lambda data set
First, we'll run breseq on a small data set to be sure that it is installed correctly, and to get a taste for what the output looks like. This sample is a mixed population of bacteriophage lambda that was co-evolved in lab with its E. coli hosts.
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breseq access
In order to run breseq, we need to make sure breseq was made available to you when we set up your .bashrc file on the first day.
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tacc:~$ which breseq # expected output: /corral-repl/utexas/BioITeam/breseq/bin/breseq tacc:~$ breseq --version # expected output: breseq 0.35.1 |
breseq should should now run using the the breseq command command. breseq without without any options will show you what the command expectations are.
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| Not all programs are configured to tell you what it expects just from typing the name of it. Some require the name of the command followed by one of the following: -h or --help or ? while others require preceding the command name with "man" (short for manual). If all that fails google is your friend for all programs not named "R" ... google is still your best bet, but it won't be your friend. In the specific case of R, adding the word stats somewhere to the search will greatly help things in my experience. |
Bacteriophage lambda data set
First, we'll run breseq on a small data set to be sure that it is installed correctly, and to get a taste for what the output looks like. This sample is a mixed population of bacteriophage lambda that was co-evolved in lab with its E. coli hosts.
Data
The data files for this tutorial is located in following location:
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