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While you could consult previous year's tutorial for installing bowtie2 via the module system, this year's course will be using the conda system to install it. The bowtie2 home page can be found here, and if you needed to download the program itself, version 2.45.5 could 1 could be downloaded here. Instead, we want to make sure the bowtie2 version 2.45.5 1 is installed via conda Like we did for fastqc and cutadapt. See if you can figure out how to install bowtie2 into a new conda environment named "GVA-bowtie2-mapping". Note that "2" is actually part of the program name, neither a typo nor a comment on the program version.

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• In the bowtie2 example, we mapped in --local mode. Try mapping in --end-to-end mode (aka global mode).

• Do the BWA tutorial so you can compare their outputs (note BWA has a conda package making it even easier to try).
  • Did bowtie2 or BWA map more reads?
  • In our examples, we mapped in paired-end mode. Try to figure out how to map the reads in single-end mode and create this output.
  • Which aligner took less time to run? Are there any options you can change that:
    • Lead to a larger percentage of the reads being mapped? (increase sensitivity)
    • Speed up run time without causing many fewer reads to be mapped? (increase performance)

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