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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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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 newdo not need to install a compiler (GCC/ICC), bowtie2, or R on TACC as they are available via the module system.
You could add these commands to your $HOME/.profile_user if you wanted them available by default. |
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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 Code Block | |
Example 1: Bacteriophage lambda data set
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