We are going to use the BWA-mem aligner to align reads to the human genome, version hg38.

1. Select the BWA-MEM tool in the Galaxy tool bar

   

2. Fill carefully the tool form

   Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome (Galaxy Version 0.7.17.1)

   • Will you select a reference genome from your history or use a built-in index?: Use a built-in genome index
   • Single or Paired-end reads: Paired Collection
     • Select a paired collection: A or B collection
     • Enter mean, standard deviation, max, and min for insert lengths.: 280
   • Set read groups information?: Do not set
   • Select analysis mode: 1. Simple Illumina mode

   This should give you a form similar to:

3. Click the Execute button