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  • Haploid reference genome
  • Relatively small (<20 Mb) reference genome
  • Input FASTQ reads can be from any sequencing technology
  • Average genomic coverage > 2030-fold
  • Less than ~1,000 mutations expected
  • Detects SNVs and structural variants SVs from single-end reads (does not use paired-end distance information)
  • Produces annotated HTML output

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See if you can install breseq and get it running from the installation instructions.

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Info
titleInfo for installing breseq on TACC

You

will need Bowtie version 2.0.0-beta7 or later to run breseq. The version available on TACC by module laod is currently not this new

do not need to install a compiler (GCC/ICC), bowtie2, or R on TACC as they are available via the module system.

Code Block
module load R

module load GCC
module load bowtie/2.1.0

You could add these commands to your  $HOME/.profile_user if you wanted them available by default.

module load R

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I need help...
I need help...

Hint: The previous lesson We have some optional info on Installing Linux tools that should help you get bowtie2 and breseq installed. A suitable version of R is already installed on TACC. Remember that you can load that using the command:

Code Block

Example 1: Bacteriophage lambda data set

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